ME TOO! i wish there was a fix, but no one has come up with one that actually works for me. i assume this problem is occuring across the board for gmail users. at least, ive read over 20 posts (here and other sites) with the same complaint. im sure google (or Apple) will release an update to fix this.
i hate to say it, but never had this problem on BB. it only downloaded new unread emails. the iPhone downloads every email ive ever had always keeping my inbox FULL. its annoying, but at least all new emails still make it to me.