My bet would be that the system time is based on GMT and then the .xinitrc for the user has a timezone argument and no LIBPATH while the .bash_profile or .bashrc has no timezone argument but does have a LIBPATH. Your description is somewhat sketchy to make this leap but my conclusion is based on the fact that Exceed starts an X session and KEA Term just gives you a terminal session. In the terminal session (assuming you are using bash) your login would cause the .bash_profile to be run (using ksh it would be the .profile). These are things that I would check if I were hunting that one down.
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