I just switched our SSL certificates to newer ones (they used intermediate
certificates before as well). Before, I didn't need to accept or save the
certificates as long as $ssl_ca_certificates_file was set to the system bundle
(which has at least the root certificate in the chain, based on the
fingerprint). Since upgrading, though, I'm prompted to accept *all*
certificates in the chain when connecting via IMAP.

Does the extra "anchor" cause a problem, or is there some other problem I'm
missing?

The chain, as reported by openssl s_client -connect [host]:993:

Certificate chain
 0 s:/C=US/postalCode=XXXXXXXX
   i:/C=US/ST=MI/L=Ann Arbor/O=Internet2/OU=InCommon/CN=InCommon RSA Server CA
 1 s:/C=US/ST=MI/L=Ann Arbor/O=Internet2/OU=InCommon/CN=InCommon RSA Server CA
   i:/C=US/ST=New Jersey/L=Jersey City/O=The USERTRUST Network/CN=USERTrust RSA 
Certification Authority
 2 s:/C=US/ST=New Jersey/L=Jersey City/O=The USERTRUST Network/CN=USERTrust RSA 
Certification Authority
   i:/C=SE/O=AddTrust AB/OU=AddTrust External TTP Network/CN=AddTrust External 
CA Root
 3 s:/C=SE/O=AddTrust AB/OU=AddTrust External TTP Network/CN=AddTrust External 
CA Root
   i:/C=SE/O=AddTrust AB/OU=AddTrust External TTP Network/CN=AddTrust External 
CA Root

$ mutt -D | egrep "ssl|certificate"
certificate_file="~/.mutt_certificates"
smime_certificates=""
ssl_ca_certificates_file="/etc/pki/tls/certs/ca-bundle.crt"
ssl_client_cert=""
ssl_force_tls is unset
ssl_min_dh_prime_bits=0
ssl_starttls=yes
ssl_use_sslv3 is set
ssl_use_tlsv1 is set
ssl_verify_dates is set
ssl_verify_host is set

$ mutt -v
Mutt 1.5.20 (2009-12-10)
Copyright (C) 1996-2009 Michael R. Elkins and others.
Mutt comes with ABSOLUTELY NO WARRANTY; for details type `mutt -vv'.
Mutt is free software, and you are welcome to redistribute it
under certain conditions; type `mutt -vv' for details.

System: Linux 2.6.18-400.el5 (x86_64)
ncurses: ncurses 5.5.20060715 (compiled with 5.5)
libidn: 0.6.5 (compiled with 0.6.5)
hcache backend: Sleepycat Software: Berkeley DB 4.3.29: (May 26, 2010)
Compile options:
-DOMAIN
-DEBUG
-HOMESPOOL  -USE_SETGID  +USE_DOTLOCK  -DL_STANDALONE  +USE_FCNTL  -USE_FLOCK   
+USE_POP  +USE_IMAP  +USE_SMTP  
-USE_SSL_OPENSSL  +USE_SSL_GNUTLS  +USE_SASL  +USE_GSS  +HAVE_GETADDRINFO  
+HAVE_REGCOMP  -USE_GNU_REGEX  
+HAVE_COLOR  +HAVE_START_COLOR  +HAVE_TYPEAHEAD  +HAVE_BKGDSET  
+HAVE_CURS_SET  +HAVE_META  +HAVE_RESIZETERM  
+CRYPT_BACKEND_CLASSIC_PGP  +CRYPT_BACKEND_CLASSIC_SMIME  -CRYPT_BACKEND_GPGME  
-EXACT_ADDRESS  -SUN_ATTACHMENT  
+ENABLE_NLS  -LOCALES_HACK  +HAVE_WC_FUNCS  +HAVE_LANGINFO_CODESET  
+HAVE_LANGINFO_YESEXPR  
+HAVE_ICONV  -ICONV_NONTRANS  +HAVE_LIBIDN  +HAVE_GETSID  +USE_HCACHE  
ISPELL="/usr/bin/hunspell"
SENDMAIL="/usr/sbin/sendmail"
MAILPATH="/var/mail"
PKGDATADIR="/usr/share/mutt"
SYSCONFDIR="/etc"
EXECSHELL="/bin/sh"
-MIXMASTER
To contact the developers, please mail to <mutt-...@mutt.org>.
To report a bug, please visit http://bugs.mutt.org/.

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