Hi,
   In reply to my own mail, I have found the answer to it, in case anyone is
interested.
   Well, it is not a problem of the Xserver, neither of the other programs.
Rather,it was a problem of Mesa 2.3. Now that 2.4 is out, I compiled it and all
problems are gone. Now vtk, vis5d, glchess and almost all programs that didn't
work before work now. There are a few that still don't work but there probably
is a solution for this...
   So I would suggest that anyone who uses Mesa on NetBSD go and get 2.4.

PS. Does anyone use either MuPad or Scilab?

-- 
Konstantinos Margaritis
Under-graduate student at Physics Dept. of Athens University
e-mail: markos@acropolis.net, talk: root@markos.dyn.ml.org