For those of us who use gmail, the new update brings one feature I could do without, it determines unread from gmail, not from what is on the phone itself.
To fix you can follow the instructions here http://www.zdnet.com/blog/btl/how-to-mark-all-unread-emails-as-read-in-gmail-and-more/80754
Got whacked by having thousands of unread indicators. I read mail primarily on my phone but my Mac also grabs mail from there. So while the Mac is only counting what it knows to be unread in its local mailbox the iPhone is showing what the provider claims
To fix you can follow the instructions here http://www.zdnet.com/blog/btl/how-to-mark-all-unread-emails-as-read-in-gmail-and-more/80754
Got whacked by having thousands of unread indicators. I read mail primarily on my phone but my Mac also grabs mail from there. So while the Mac is only counting what it knows to be unread in its local mailbox the iPhone is showing what the provider claims