Apparently there is a big incompatibility between GlDirect 3.0 (an OpenGl to DirectX "emulator" from http://www.scitechsoft.com) and Dos games.
GlDirect requires you to start up gldirect.exe to use it (normally done per autostart in the registry). If it has been run (even if gldirect is disabled in its settings) all Dos games freeze once they run fullscreen.
Even Dos applications like Norton Commander freeze when run fullscreen.

I submitted a bug report to scitechsoft and the support person could reproduce it so I guess this issue is being looked at.

So just for everyone to take notice if they are using GlDirect.