The way I see it there are two possibilities:
1. They went through the votes and threw out the ones where there were 10,000 for (pokemon) from a single IP to prevent the vote spammers/scripters from having their way.
or
B. The poll was rigged for a legendary to win from the start.
Once they reveal the runners up we can tell which one it is, if Mudkip is in the top three then we know the scripts worked, if it isn't then we know whoever is in charge of the poll actually fixed the problem of vote spamming.
There is a third, albeit much less likely possibility: that a lone wolf or a small group who did not vocalize their fiendish plot figured out a script to spam arceus early on and singlehandedly highjacked the pole.