Mine did this, then it would make odd noises, then it took ages to wake from sleep, then it took many attempts to get it to boot up and then finally it wouldn't boot at all. The HDD failed and it's currently at Apple being replaced. According to them it's a very common problem and even though mine is under warranty they said they would have done it out of warranty anyway as it happens a lot.
Disk Utility or the Apple hardware test never showed any problems for me either which is odd, as it was clearly failing.
Is yours a WD HDD?