I've got more ideas but more info would help,maybe some code.I got it working pretty darn well using bsp's made with the Hammer editor and Zoner's tools so i'll just throw some things bye ya.
What grafix card are you using?I had some trouble with my mx400 64meg till i reinstalled the latest nvidia driver.
Be sure you have the latest grafix drivers installed properly.
what kind of bsp?Quake,Half-Life or DBP bsp?
Could be your collision code.Could be a bad compile.What are you compiling the Bsp file with?Make sure the map is clear of overlapping primitives as that seemed to mess things up.Was a thread here somewhere,i think it was called ultimate bsp thread but i can't find it.You may find something useful in it.I don't want to discourage you but most can't get past setting up Hammer before they give up entirely.
OC`ed AMD 2.2Ghz/1GB DDR ram/GeForce Fx5200 128MB/1Mb cable/W2KPro/DBPro/Updated.