Why won't mail.app get my most recent messages?

So, I’ve configured mail.app to work with my alternate email address (thanks fluther!), but now mail won’t sync my newest email messages through POP… even though i have done this in the past and my iPhone syncs just dandy. To make matters worse, I fiddled with the “archive messages after they’re downloaded” setting on gmail, and now mail is downloading archived mail from 2005!