After game start (in 3dfx mode) desktop and all icons that ware displayed on the first monitor are swapped with desktop from monitor 2 and it kees that way even after quiting the game... (computer restart did not fix it)

Any1 encountered similar or even same problem, any ideas?

Try dgVoodoo and see if it happens with that. There's a dropdown box in dgVoodooCpl.exe that allows you select which monitor to use for the game. See my guide for help setting up dgVoodoo.

Why not disable your monitor with win+P before you start the game? Problem solved.