I've been keeping a list of IGMC game ratings since the start (rating amount, the only thing that is public info) for my own amusement (I like statistics) and gotta say, things have been rather weird :D
Viewing post in Rating irregularities
Yes; my thought is the 'popular' vote thing probably won't be accurate or fair really and (IMHO) probably shouldn't be a thing for future IGMC contests. For $5,000, people will be tempted to cheat and fudge and votebot and all manner of stuff. It comes down more to marketing rather than what the best game really is, which shouldn't be the point of a IGMC.
The judges have mentioned in other threads that it -IS- about marketing (and that's not a bad skill to have especially in the current state of indie games where there's lots of games fighting for attention. It along with social networking are essential.) This isn't the first time IGMC has had a voting component, I'm sure the organizers know well enough to watch for any suspicious activity, bots, or duplicate accounts and such. Especially on games in the running for the top 3.