Yes, you will even see those you not supposed to see (hidden files).

I think you are running low in space. You can try reduce your windows partition size.
I had this problem before when my HDD running in tight free space.

Yeap, if more space doesn't help next is to try disk repair tools like disk warrior, drive genius or techtool pro.
Last is to clone or install to external.

Have you try re-applying last OSX update?

This post has been edited by wei: Mar 19 2010, 10:44 PM

Yes, this issue happen on those that upgrade from 10.5 -> 10.6 most of the time.
Time Machine will do a roll-back for you, so it's not entirely clean.

By clean means wipe your HDD clean by re-partitioning/re-formatting. Then install the Mac OSX from the installer, apply all required OSX/software update from Apple. Finally install Apps you need and move back your files (but not your user folder entirely).

Have you try create a new user and partition from there? Just another try before you spend hours to reconfigure everything.

Glad it worked for you.