I had the same issue for the first time during this past month. Was driving me nuts that MAIL was showing an "unread" email, but I could not identify or locate it.
I did the REBUILD and the culprit went away . . . er, at least on my desktop computer. An "unread" indicator still shows up, however, when I open my MAIL on my IPAD.
Any ideas how also to clean up the MAIL APP on the iPAD?