Unfortunately since Apple released a support article about the issue, I'm thinking it sadly might be "as designed' and not a bug afterall
http://support.apple.com/kb/TS1795
Thats my exact problem: Lets say I check 3 new e-mails on my computer, when I pick up my iPhone 5 hours later, if I didn't receive any new e-mail since that time, my iPhone will STILL show 3 unread e-mails. Only when I enter the app and it fetches from the server will it update.
I think the issue lies in the fact that the read/unread status is not push, its pull only. The only way to solve it right now is to set Mobile Me to Push AND Pull, which is BS.
So far Mobile Me feels like a poorly implemented hodgepodge of IMAP & Push, and sadly I'm very disappointed.