I had this same issue with a Yahoo account. After the iOS7 update it started showing showing i had 16 unread messages but when i logged in on my computer i only had 3 in my inbox and they weren't unread. Previous to that i had also cleared out every other folder to make sure it wasn't anything in there.
This is what i did to finally get it to get rid of the ghost unread messages:
Settings > Mail > Yahoo (or whatever your troubled account is) > Account: > SMTP > Primary Server > Server = off.
I backed out once screen and went into Advanced > S/MIME = On, left everything else under that as whatever the default was.
I backed out all the way to the home screen and went back in to turn on the SMTP Primary Server. When i backed out the 2nd time, the ghost messages were gone!
I'm not 100% sure what the S/MIME does or if it even helped clear the issue but since I didnt check right after i turned the server off i'm gonna assume it was also part of the solution.
Hope that helps someone out there!