I am running Popularity Contest 1.2.1 and the latest WP. I noticed that certain posts are listed twice in the Most Popular list in my sidebar. Looking into it further, I discoved that the two posts that are duplicated in the listing are also the only two that have two categories instead of one.
The list in the admin panel lists each post only once, so presumably the database is OK.
Here's what I have in my sidebar:
<?php akpc_most_popular($limit=9); ?>
This seems to be a bug. I hope that this is the best way to support it.