Get a Mac and you won't have to worry about that problem!
Seriously, I agree with Celegorm that re-installing might help, or that it may just be a beta thing. I assume that you probably have the 3.0.4 update? If you do decide to re-install it, then there is probably an easy way to save the bookmarks to your desktop and then import them back into Safari when you're done. In Mac, the bookmarks are in a file called Bookmarks.plist. It is in the safari folder that's inside the library. I can't tell you where it would be on a PC without looking at one, but I'm sure that it's not very hard to find.