That's a pretty big assumption you're making there. You can't see your current up to date PageRank, only your toolbar
PR, which Google exports once every 3 months or so. As it happens Google just recently updated Toolbar
PR, so it's no surprise you're seeing changes - however these changes are based on many different factors over the last 3 months or so. The new feature of All in One is only about a week old. It's very unlikely that it would have had much impact in that small amount of time.
That said, it would seem that people should be careful about this issue if they run WordPress in a subfolder. It may have impact on such sites, so if there's any doubt, don't use that feature of the plugin. However, it's a real stretch to blame All in One for your PageRank drop (not that PageRank matters much any more).