My theory is multi-fold: 1.)  perhaps starting hill training too early in his training camp (they said he did it on the first day or first week of training)  2.)  he seemed to work WAY more with Alex Ariza than before.  On top of that there was a week when Freddie Roach left the camp and Pacquiao worked ONLY on conditioning and strengthening for that whole week.  3.)  Mosley's body punches.  I feel putting in too much muscle and body work during training camp can hinder smooth movement and short bursts of explosiveness in fights over a long period of time.  I feel all that muscle work takes away some of the natural flexibility of muscles and the natural grace needed in boxing (hand work, footwork, punching, dipping and slipping).  My other theory is that perhaps Mosley's body punches took effect on Pacquiao in the later rounds. 

Random Rant ** :

However, it is to be noted Pacquiao was flat footed from the beginning.  Was that part of his game plan to not do the usual:  jab, left cross, move the right of the opponent and throw combination the way he did with Cotto?  Perhaps they were avoiding Mosley's left hook, and thought that Pacquiao's left cross (very straight and fast) would nullify Mosley's overhand right (which he didn't use, all of his right hands were straight right crosses).  On top of that, Mosley was circling away from the left hand, which is what Morales and Marquez did.  Pacquiao should have stepped to his right to cut off the ring, and then throw a left cross to stop him in his tracks.  Pacquiao can't pressure and cut off the ring, maybe something Mayweather might notice.  Anyway, excuse the last part, it was just a rant.  Holler!