Well, the only problems I ever had with zDoom were on a machine with a flatscreen. Switching to 320x200 mode made the screen go black. But other than that... No, never any problems. Which version are you using? And more importantly: did you report it at the zDoom forums?
Did you ever try any doom wads like
ColdAsHell or the
zDoom Community Map?
If you did - show me another port which can do THAT. Not just 3d-models for monsters, but NEW monsters. Not just "high res" textures but slopes and scripts, scripts, scripts...
BTW: There's also a
zDoomGL for those who really need it.
