When diagnosing problems like these, it helps to backup your data and reflash to stock. If it is a hardware problem it will persist from that point. That being said, I can think of a few hardware things that would cause it. Having torn down my N900 to bare plastic twice to replace the LCD then the digitizer (touch screen panel), I've noticed quite a bit of less-than-stellar engineering.

Do you have these problems with the screen when the screen is slid up (keyboard exposed)? The flex cable is very fragile - I've torn one. The display would act fine with the keyboard open, but once it was closed it'd go nuts.

Start by reflashing, then just poke around and see if you can replicate it if the problem persists. If you need any assistance, send me a message. Cheers!