I have more to report on this problem.
 
I am using current stable:
kernel - 1.1.35 Build 2035b-cvs, 2006-05-21
freecom - 0.84-pre XMS_Swap, 2006-05-21
himem + emm386 - from emmx208 or emm208x ZIP archive
 
I might have added to the original post by saying that this problem does not occur on an older 486 SX2-50 (no math coprocessor) in an ISA-only motherboard.  Only on this newer Pentium 100 with PCI + ISA.
 
I could also have added that all my DOS games (Doom, Quake, Duke, Spacequest, Beneath A Steel Sky) run fine on this computer and configuration.
 
On the chance that there was a physical memory problem I dropped from 16 to 8 MB (no difference), and then also swapped in the extra 8 MB (no difference).
 
One thing I noticed in further testing was that Draw, Paint and Doodle have the most problems.  All freehand programs.  And if they load successfully, then they work until you try to close them.  Artline is rather stable by comparison, though it does not seem to offer a freehand tool, at least that I could find quickly.
 
If I drop all the way to no HIMEM and no EMM386, there is insufficient memory to run Artline or Paint.  Draw, Write, Tetris, Scgem, and Fanwor all seemed to work.  But Doodle locks the machine when it closes.
 
If I add back HIMEM but not EMM386, Doodle causes a reboot while it is loading.  And Write and Draw lock up the machine while loading.
 
If I add back HIMEM and EMM386, Doodle, Draw and Paint all lock up the machine while closing.
 
I saw a thread (March?) in the OpenGEM-dev list that for the OpenGEM/XM project, there was a user who, when he was running more than one GEM app with graphics under FreeDOS, there was some kind of interference.  The opinion there was that the problem was traceable to the FreeDOS kernel, because the problem did not occur with a couple of other DOS kernels.  This sort of behavior seemed related to what I am experiencing on this computer.
 
--John Hupp
 
P.S. my test config & autoexec, further simplified from the originally reported configurations - more mod reports above:
 
LASTDRIVE=Z
BUFFERS=30
FILES=40
DOS=HIGH,UMB
DEVICE=C:\FDOS\BIN\HIMEM.EXE
DEVICE=C:\FDOS\BIN\EMM386.EXE NOEMS X=TEST VDS
SHELL=C:\command.com C:\ /E:512 /P=C:\AUTOEXEC.BAT
------------------------------------------------------------------------------------------
SET PROMPT=$P$G
SET DOSDIR=C:\FDOS
SET PATH=C:\NET;C:\;C:\FDOS\bin;C:\DOSSHELL;C:\PKZIP
SET TEMP=C:\FDOS\TEMP
SET TMP=C:\FDOS\TEMP
 
CTMOUSE

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