So can you play through games not in 3d? When did you first notice this issue? If it used to work but stopped recently, obviously any changes on your machine like updating your OS would be useful to know.
I'd suggest playing around with 3d options to see if you can narrow it down. Basically, go through all the 3d settings both on the game page as well as the 3d settings from the settings popup (File->Settings, the one with various tabs like facegen and troubleshooting), turn everything off or to the min settings, and then see if that works.
The other big option that can affect things are the openGL settings. There's a dropdown with options like "always use openGL", "use openGL and Fast Blit", etc... Let us know which of those settings you're using, and if you can, trying a different setting may help.
Hopefully something in here is an easy fix for you. If none of these work, then I would suggest continuing the debugging through our support portal (
https://support.ootpdevelopments.com/portal/home) where they may have other suggestions or options to check and try.