The best theory I heard was that, eventually, the ground became so tightly packed and airless that Jack's body was unable to revive fully when it came back to life, so he spent the majority of the time pretty much unconscious. Which helps SOME, but still. STILL.

AND NOTHING EXPLAINS THE CLOTHES. GOD I hated most of that episode. If not for the amazing powers of Burn Gorman and Naoko Mori, it would have been completely worthless.