I had the same issue since 2.36! heres what happened to me. I played MGS4,had some issues with MGO so I had to reboot my PS3. Upon rebooting my PS3 I received a message that said "Your filesystem is corrupt and needs to be restored."
Upon attempting to restore the filesystem the system would crash at 40%! This happened 3 times on my 250gb HDD. Then I put in the old 120gb HDD! It happened 2 more times on that HDD.
I then tried to boot up yet another 120gb HDD, which I acutally took from a computer that fell and displayed an error message (on the computer) which said my HDD was corrupted. Oddly enough, it was this HDD that worked.
I said it before in a post awhile ago, and ill say it again. The PS3 has a serious hardware issue, but I think they are covering it up. A bluetooth headset, network errors, GTAIV, firmware updates. THIS SHOULDN'T BE CAUSING SUCH HUGE SYSTEM FAILURES! If it wasn't for my persistence with my PS3 I would have sent out my PS3 in a $150 UPS box by now and been waiting on Sony to return it.
God knows I love my PS3, but there is something seriously wrong with the hardware somewhere in there.