Via Primer, this is a cool article that attempts to explain the differences between Jason Bay in 2006 and Bay in 2007 by using video to demonstrate differences in his swing. It's all very anecdotal, but the general idea is believable, and here it is: the 2007 Bay was having mechanical problems in that he wasn't planting his foot and rotating his hips in a seamless way.
I don't feel overly qualified to comment too much on this kind of thing, but you should take a look at the video and let me know what you think. The author never really makes the connection, but his observation about Bay's alleged mechanical problems is consistent with the possibility that most of Bay's struggles resulted from his left knee injury. If the knee was bothering him, it might have caused a hitch in his foot plant that would prevent him from generating power with his hips.