>What were your configure options?  

./configure --enable-rebuild-tcpserver-file=n --enable-roaming-users=y
--enable-defaultquota=20971520S --enable-auth-module=mysql
--enable-file-sync=n --enable-mysql-logging=y --enable-learn-passwords=y
--enable-clear-passwd=y --enable-valias=y --enable-mysql-limits=y
--enable-logging=p --enable-relay-clear-minutes=15

>What does your config.h file look like?  This is very odd, and something
that I haven't seen before.

/* config.h.  Generated automatically by configure.  */
/* config.h.in.  Generated automatically from configure.in by autoheader.
*/

/* Define if the closedir function returns void instead of int.  */
/* #undef CLOSEDIR_VOID */

/* Define to empty if the keyword does not work.  */
/* #undef const */

/* Define to `int' if <sys/types.h> doesn't define.  */
/* #undef gid_t */

/* Define if you have <sys/wait.h> that is POSIX.1 compatible.  */
#define HAVE_SYS_WAIT_H 1

/* Define if utime(file, NULL) sets file's timestamp to the present.  */
#define HAVE_UTIME_NULL 1

/* Define as __inline if that's what the C compiler calls it.  */
/* #undef inline */

/* Define to `int' if <sys/types.h> doesn't define.  */
/* #undef mode_t */

/* Define to `long' if <sys/types.h> doesn't define.  */
/* #undef off_t */

/* Define to `int' if <sys/types.h> doesn't define.  */
/* #undef pid_t */

/* Define as the return type of signal handlers (int or void).  */
#define RETSIGTYPE void

/* Define to `unsigned' if <sys/types.h> doesn't define.  */
/* #undef size_t */

/* Define if you have the ANSI C header files.  */
#define STDC_HEADERS 1

/* Define if your <sys/time.h> declares struct tm.  */
/* #undef TM_IN_SYS_TIME */

/* Define to `int' if <sys/types.h> doesn't define.  */
/* #undef uid_t */

/* Define if you have the bzero function.  */
#define HAVE_BZERO 1

/* Define if you have the dup2 function.  */
#define HAVE_DUP2 1

/* Define if you have the fdatasync function.  */
#define HAVE_FDATASYNC 1

/* Define if you have the getcwd function.  */
#define HAVE_GETCWD 1

/* Define if you have the gethostname function.  */
#define HAVE_GETHOSTNAME 1

/* Define if you have the getpass function.  */
#define HAVE_GETPASS 1

/* Define if you have the getspnam function.  */
#define HAVE_GETSPNAM 1

/* Define if you have the memset function.  */
#define HAVE_MEMSET 1

/* Define if you have the mkdir function.  */
#define HAVE_MKDIR 1

/* Define if you have the putenv function.  */
#define HAVE_PUTENV 1

/* Define if you have the rmdir function.  */
#define HAVE_RMDIR 1

/* Define if you have the socket function.  */
#define HAVE_SOCKET 1

/* Define if you have the strchr function.  */
#define HAVE_STRCHR 1

/* Define if you have the strdup function.  */
#define HAVE_STRDUP 1

/* Define if you have the strerror function.  */
#define HAVE_STRERROR 1

/* Define if you have the strncasecmp function.  */
#define HAVE_STRNCASECMP 1

/* Define if you have the strrchr function.  */
#define HAVE_STRRCHR 1

/* Define if you have the strspn function.  */
#define HAVE_STRSPN 1

/* Define if you have the strstr function.  */
#define HAVE_STRSTR 1

/* Define if you have the utime function.  */
#define HAVE_UTIME 1

/* Define if you have the <arpa/inet.h> header file.  */
#define HAVE_ARPA_INET_H 1

/* Define if you have the <dirent.h> header file.  */
#define HAVE_DIRENT_H 1

/* Define if you have the <fcntl.h> header file.  */
#define HAVE_FCNTL_H 1

/* Define if you have the <memory.h> header file.  */
#define HAVE_MEMORY_H 1

/* Define if you have the <ndir.h> header file.  */
/* #undef HAVE_NDIR_H */

/* Define if you have the <netinet/in.h> header file.  */
#define HAVE_NETINET_IN_H 1

/* Define if you have the <shadow.h> header file.  */
#define HAVE_SHADOW_H 1

/* Define if you have the <stdlib.h> header file.  */
#define HAVE_STDLIB_H 1

/* Define if you have the <string.h> header file.  */
#define HAVE_STRING_H 1

/* Define if you have the <sys/dir.h> header file.  */
/* #undef HAVE_SYS_DIR_H */

/* Define if you have the <sys/file.h> header file.  */
#define HAVE_SYS_FILE_H 1

/* Define if you have the <sys/ndir.h> header file.  */
/* #undef HAVE_SYS_NDIR_H */

/* Define if you have the <sys/param.h> header file.  */
#define HAVE_SYS_PARAM_H 1

/* Define if you have the <sys/socket.h> header file.  */
#define HAVE_SYS_SOCKET_H 1

/* Define if you have the <sys/time.h> header file.  */
#define HAVE_SYS_TIME_H 1

/* Define if you have the <syslog.h> header file.  */
#define HAVE_SYSLOG_H 1

/* Define if you have the <unistd.h> header file.  */
#define HAVE_UNISTD_H 1

/* Define if you have the <utime.h> header file.  */
#define HAVE_UTIME_H 1

/* Define if you have the crypt library (-lcrypt).  */
#define HAVE_LIBCRYPT 1

/* Name of package */
#define PACKAGE "vpopmail"

/* Version number of package */
#define VERSION "5.4.0-rc1"

/*  */
#define PS_COMMAND "ps axww"

/*  */
#define QMAILDIR "/var/qmail"

/*  */
#define QMAILNEWU "/var/qmail/bin/qmail-newu"

/*  */
#define QMAILINJECT "/var/qmail/bin/qmail-inject"

/*  */
#define QMAILNEWMRH "/var/qmail/bin/qmail-newmrh"

/*  */
#define VPOPUSER "vpopmail"

/*  */
#define VPOPGROUP "vchkpw"

/*  */
#define VPOPMAILDIR "/home/vpopmail"

/*  */
#define VPOPMAILUID 89

/*  */
#define VPOPMAILGID 89

/*  */
#define POP_AUTH_OPEN_RELAY 1

/*  */
#define TCPRULES_PROG "/usr/local/bin/tcprules"

/*  */
#define TCP_FILE "/home/vpopmail/etc/tcp.smtp"

/*  */
/* #undef REBUILD_TCPSERVER */

/*  */
#define RELAY_CLEAR_MINUTES 15

/*  */
#define OPEN_SMTP_CUR_FILE "/home/vpopmail/etc/open-smtp"

/*  */
#define OPEN_SMTP_TMP_FILE "/home/vpopmail/etc/open-smtp.tmp"

/*  */
#define OPEN_SMTP_LOK_FILE "/home/vpopmail/etc/open-smtp.lock"

/*  */
#define ENABLE_LEARN_PASSWORDS 1

/*  */
#define MD5_PASSWORDS 1

/*  */
#define FILE_LOCKING 1

/*  */
/* #undef FILE_SYNC */

/*  */
#define MAKE_SEEKABLE 1

/*  */
#define CLEAR_PASS 1

/*  */
#define USERS_BIG_DIR 1

/*  */
/* #undef SQWEBMAIL_PASS */

/*  */
/* #undef QMAIL_EXT */

/*  */
/* #undef IP_ALIAS_DOMAINS */

/*  */
#define HARD_QUOTA "20971520S"

/*  */
/* #undef DOMAIN_QUOTAS */

/*  */
#define VLIMITS_DEFAULT_FILE "/home/vpopmail/etc/vlimits.default"

/*  */
#define DOMAINS_DIR "domains"

/*  */
/* #undef USE_CDB */

/*  */
#define USE_SQL 1

/*  */
#define USE_MYSQL 1

/*  */
#define USE_SQL 1

/*  */
/* #undef USE_POSTGRES */

/*  */
/* #undef USE_LDAP */

/*  */
#define USE_SQL 1

/*  */
/* #undef USE_ORACLE */

/*  */
#define USE_SQL 1

/*  */
/* #undef USE_SYBASE */

/*  */
/* #undef USE_ACTIVE_DIR */

/*  */
/* #undef ENABLE_PASSWD */

/*  */
#define HAS_SHADOW 1

/*  */
#define ENABLE_LOGGING 3

/*  */
#define ENABLE_LOGGING 3

/*  */
#define ENABLE_LOGGING 3

/*  */
#define ENABLE_LOGGING 3

/*  */
#define ENABLE_LOGGING 3

/*  */
#define LOG_NAME "vpopmail"

/*  */
#define ENABLE_AUTH_LOGGING 1

/*  */
#define ENABLE_MYSQL_LOGGING 1

/*  */
/* #undef ENABLE_PGSQL_LOGGING */

/*  */
#define ENABLE_MYSQL_LIMITS 1

/*  */
/* #undef MYSQL_REPLICATION */

/*  */
#define VALIAS 1

/*  */
#define MANY_DOMAINS 1


>What does /var/qmail/users/assign look like?  
+cwispy.com-:cwispy.com:89:89:/home/vpopmail/domains/cwispy.com:-::
+bscg.com.au-:bscg.com.au:89:89:/home/vpopmail/domains/bscg.com.au:-::
+sportsturf.net.au-:sportsturf.net.au:89:89:/home/vpopmail/domains/sportstur
f.net.au:-::
+gcswa.com-:gcswa.com:89:89:/home/vpopmail/domains/gcswa.com:-::
+traxlogistics.com.au-:traxlogistics.com.au:89:89:/home/vpopmail/domains/tra
xlogistics.com.au:-::
+triviaworld.org-:triviaworld.org:89:89:/home/vpopmail/domains/triviaworld.o
rg:-::
+studioreddust.com.au-:studioreddust.com.au:89:89:/home/vpopmail/domains/stu
dioreddust.com.au:-::
+reddustmedia.com.au-:studioreddust.com.au:89:89:/home/vpopmail/domains/stud
ioreddust.com.au:-::
+thepreshrunkorganisation.com-:preshrunk.com.au:89:89:/home/vpopmail/domains
/preshrunk.com.au:-::
+bitsys.com.au-:bitsys.com.au:89:89:/home/vpopmail/domains/bitsys.com.au:-::
+rangeresources.com.au-:rangeresources.com.au:89:89:/home/vpopmail/domains/r
angeresources.com.au:-::
+primitivebodypiercing.com-:primitivebodypiercing.com:89:89:/home/vpopmail/d
omains/primitivebodypiercing.com:-::
+traditionaltattoos.net-:primitivebodypiercing.com:89:89:/home/vpopmail/doma
ins/primitivebodypiercing.com:-::
+ucanbuildit.com.au-:ucanbuildit.com.au:89:89:/home/vpopmail/domains/ucanbui
ldit.com.au:-::
+preshrunk.com.au-:preshrunk.com.au:89:89:/home/vpopmail/domains/preshrunk.c
om.au:-::
+nathancarroll.com-:nathancarroll.com:89:89:/home/vpopmail/domains/nathancar
roll.com:-::
+faceitonline.net-:faceitonline.net:89:89:/home/vpopmail/domains/faceitonlin
e.net:-::
+dhb2.com-:dhb2.com:89:89:/home/vpopmail/domains/dhb2.com:-::
+achtung.com.au-:achtung.com.au:89:89:/home/vpopmail/domains/achtung.com.au:
-::
+luxebar.com-:luxebar.com:89:89:/home/vpopmail/domains/luxebar.com:-::
+bizsolution.com.au-:bizsolution.com.au:89:89:/home/vpopmail/domains/bizsolu
tion.com.au:-::
+webbize.com-:webbize.com:89:89:/home/vpopmail/domains/webbize.com:-::
+acs-abacus.com-:acs-abacus.com:89:89:/home/vpopmail/domains/acs-abacus.com:
-::
+stratbras.com-:stratbras.com:89:89:/home/vpopmail/domains/stratbras.com:-::
+onsite.amepl.com.au-:onsite.amepl.com.au:89:89:/home/vpopmail/domains/onsit
e.amepl.com.au:-::
+kandu.com.au-:kandu.com.au:89:89:/home/vpopmail/domains/kandu.com.au:-::
+delirium.com.au-:delirium.com.au:89:89:/home/vpopmail/domains/delirium.com.
au:-::
+astop.com.au-:astop.com.au:89:89:/home/vpopmail/domains/astop.com.au:-::
+psylhusk.com.au-:psylhusk.com.au:89:89:/home/vpopmail/domains/psylhusk.com.
au:-::
+asthmastop.com-:asthmastop.com:89:89:/home/vpopmail/domains/asthmastop.com:
-::
+picton-warlow.com.au-:picton-warlow.com.au:89:89:/home/vpopmail/domains/pic
ton-warlow.com.au:-::
+christinemoro.com.au-:christinemoro.com.au:89:89:/home/vpopmail/domains/chr
istinemoro.com.au:-::
+allforms.com.au-:allforms.com.au:89:89:/home/vpopmail/domains/allforms.com.
au:-::
+paperandpens.com.au-:allforms.com.au:89:89:/home/vpopmail/domains/allforms.
com.au:-::
+palmerston.org.au-:palmerston.org.au:89:89:/home/vpopmail/domains/palmersto
n.org.au:-::
+bookstop.com.au-:bookstop.com.au:89:89:/home/vpopmail/domains/bookstop.com.
au:-::
+coffeebucket.com-:coffeebucket.com:89:89:/home/vpopmail/domains/coffeebucke
t.com:-::
+morelight.com.au-:morelight.com.au:89:89:/home/vpopmail/domains/morelight.c
om.au:-::
+sleeperwood.com.au-:sleeperwood.com.au:89:89:/home/vpopmail/domains/sleeper
wood.com.au:-::
+durhamlodge.net.au-:durhamlodge.net.au:89:89:/home/vpopmail/domains/durhaml
odge.net.au:-::
+durhamlodge.net-:durhamlodge.net.au:89:89:/home/vpopmail/domains/durhamlodg
e.net.au:-::
+centremediasolutions.com-:centremediasolutions.com:89:89:/home/vpopmail/dom
ains/centremediasolutions.com:-::
+centermediasolutions.com-:centremediasolutions.com:89:89:/home/vpopmail/dom
ains/centremediasolutions.com:-::
+e-mediasurveys.com-:centremediasolutions.com:89:89:/home/vpopmail/domains/c
entremediasolutions.com:-::
+emediasurveys.com-:centremediasolutions.com:89:89:/home/vpopmail/domains/ce
ntremediasolutions.com:-::
+nylandermotorsport.com.au-:nylandermotorsport.com.au:89:89:/home/vpopmail/d
omains/nylandermotorsport.com.au:-::
+2000cn.com.au-:2000cn.com.au:89:89:/home/vpopmail/domains/2000cn.com.au:-::
+ezysearch.net-:ezysearch.net:89:89:/home/vpopmail/domains/ezysearch.net:-::
+jonas.net.au-:jonas.net.au:89:89:/home/vpopmail/domains/jonas.net.au:-::
+envirokleenproducts.com.au-:envirokleenproducts.com.au:89:89:/home/vpopmail
/domains/envirokleenproducts.com.au:-::
+swim.net.au-:swim.net.au:89:89:/home/vpopmail/domains/swim.net.au:-::
+swanmari.wa.edu.au-:swim.net.au:89:89:/home/vpopmail/domains/swim.net.au:-:
:
+creativeimpressions.com.au-:creativeimpressions.com.au:89:89:/home/vpopmail
/domains/creativeimpressions.com.au:-::
+stass.com.au-:stass.com.au:89:89:/home/vpopmail/domains/stass.com.au:-::
+auscricket.net-:auscricket.net:89:89:/home/vpopmail/domains/auscricket.net:
-::
+mastastroke.com.au-:mastastroke.com.au:89:89:/home/vpopmail/domains/mastast
roke.com.au:-::
+mastastroke.com-:mastastroke.com.au:89:89:/home/vpopmail/domains/mastastrok
e.com.au:-::
+surepointsecurities.com-:surepointsecurities.com:89:89:/home/vpopmail/domai
ns/surepointsecurities.com:-::
+portrobe.com-:surepointsecurities.com:89:89:/home/vpopmail/domains/surepoin
tsecurities.com:-::
+spicemine.com.au-:spicemine.com.au:89:89:/home/vpopmail/domains/spicemine.c
om.au:-::
.


>Do the directory names match the ones you just listed?
Yes the directories are correct except that its creating the dir with
gibberish and duplicating
the directories under that.

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