I am using Windows Live Mail on Surface Pro and Windows 8.1 OS. Periodically the WLM live tile shows an unread message(s), but when I check the folders contents there are no unread messages in them. I traced these occurrences to Junk mail messages addressed to one of the IMAP accounts, however these messages do not show up in the corresponding Junk Mail folder. As a result I can not delete these messages and the only way to reset the Unread Message counter is to remove this account from my PC and add it on again. And, of course, this workaround works only until I receive another junk message.
Reinstalling the whole mail app did not help.