It sounds like this could be a number of things, but I'll take a stab at it.
The OSX filesystem is not the best as was so recently and not so subtly pointed out by Linux Torvalds, and it sounds like that might be the problem... especially since you say re-installing Safari with Pacifist fixed it. I'd recommend at least running Tech Tool Pro or Disk Warrior on your drive before you go with a reformat. Heck, even give the bundled Disk Utility a go before you shell out for those utilities, it just isn't as thorough.
The OSX filesystem is not the best as was so recently and not so subtly pointed out by Linux Torvalds, and it sounds like that might be the problem... especially since you say re-installing Safari with Pacifist fixed it. I'd recommend at least running Tech Tool Pro or Disk Warrior on your drive before you go with a reformat. Heck, even give the bundled Disk Utility a go before you shell out for those utilities, it just isn't as thorough.