Before anyone gets up in arms and starts shouting... I doubt my own theory to be true, however... some things don't add up...
First, I'm more and more convinced that the Marauder's Map is a key factor. I actually believe that it's a Horcrux more and more... One of the reasons that it can't be is because of Lupin saying they wrote it... But what if he's lying? If he is lying... then why? And then it all starts to come together...
Moony, Wormtail, Padfoot and Prongs... Lupin, PP, Sirius, and James... The order suggests that Lupin was the one who came up with it, but what if...
What if he found the Map and they merely enchanted it to be unreadable? That map is a seriously powerful object, and I find it hard to believe that a bunch of Hogwarts students, however talented, could master the magic behind that if they took nearly 5 years to master their animagus forms. Wouldn't the teachers all have such a map if it were that easy?
Even Snape thought it must have dark magic associated with it... and rarely does such a line like that make the movies if it's not significant.
So Lupin was influenced along with PP by Voldy, through the original voice of the map... Voldemort's... To quote Arthur Weasley "How many times have I told you not to talk to something if you can't see where it keeps it's brain?"... The diary got Ginny... who knows what happened when Lupin found the map?
OK, so then I start going over all the things Lupin did along the way... How is it possible that he didn't see PP in on the map earlier than the whomping willow incident in PoA... How could he forget his potion on THAT night? How could he excuse not telling DD that Sirius was an animagus? He always gives explanations that are just ok, but we accept it because he's likable (because Harry likes him)...
But here's the kicker... Every DADA teacher did something unforgiveable to us, except him... From a literary standpoint, this level of inconsistency is structurally problematic, and JKR's structure has been almost flawless throughout the series... Is the point-of-view through which we see him clouded by Harry's need to connect to his dead parents?
Ok... now there are a few more things involved, but I'll stop for now...
Yes, I admit it's pretty ludicrous for loveable Lupin to be a bad guy, but I'm just saying, if you think about it, it's not entirely IMpossible...