I've got the 2001 lectures and the 2005 lecture notes. I'm using them together - that is, listening to the lectures while keeping the lecture notes open in front of me. I can appreciate the differences because the lectures follow the 2001 notes line by line. From what I've done so far (only physio and biochem) there are very minor differences that are more like tweaking rather than actual editing. In any case, if you're going for the online Qbank, any new things you really need to know should be covered because the Qbank is pretty comprehensive and always up to date. Bottom line is if you do the Kaplan notes very well, there's no reason you'd be deficient, regardless of which edition you're using.
Question would any of you use the kaplan review books from 2000? is there really THAT big of a difference?!?