I finally got Mozilla 1.4 to work for all users on the Linux box yesterday. I think the problem was the shell script I was running for the final setup wasn't working correctly. I didn't find out until I tried to debug the script and noticed it was evaluting a function incorrectly. I hardcoded the answer and ran the script again. I had to kill the vncserver session for it to take effect.
Since I was using mc on the redhat box I decided to install mc on my cygwin installations. To get it to display correctly I had to add codepage:oem on the cygwin environmental variable. To fix the annoying cannot create temporary directory … problem I had to change the read-write privileges on the tmp directory in the cygwin folder.