I believe the reason they allow multiple votes online is because fans can vote multiple times in stadium. I went to 5 Jays games and would have been able to fill out as many ballots as I would have wanted to.
Also, it should be noted that Jason Bay was able to garner so many votes because he was the lone Canadian on the ballot, same reason Ichiro and Yao Ming (Basketball) are able to get so many votes. Basically, Jason Bay has double the home filed advantage because he has Pittsburgh and then an entire nation of baseball fans.
It should also be considered that in May, the month when the most voting was probably done, Bay hit .321, with 12 HR and 35 RBI.
I just have to believe that there is more going on here than a rock the vote campaign and a flawed voting system.