Would it help to delete any "Invisible" faces (The bottom faces of a house)
I wouldn't recommend that. The engine is culling them away anyways.
Im running several C_scans at once in different entities
Ouch. This will eat up quite some time. How long does the function execution take in milliseconds?
my menu consists of 1 800x600 panel, with about 50 64*64 panels sharing the same bmap, and have about 30 other panels visible / invisible
How long does the rendering of the panels take in milliseconds? Panels can significantly slow down rendering dependent on their number and complexity.
Video_mode is 800x600
video_depth reduced to 16 (not sure if that makes a difference)
That is really not state of the art any longer.
207 Functions running (is that bad?)
That does not matter. It's the time these function take to execute that matters.
Why don't you post a screenshot including the debug panel? That would really make things easier.