1. Let me ask you this: Do you have text under your "New Message" in email?
Compose windows no longer allow you to add icon and text. I dislike this myself. Report it to Apple Feedback so it can be logged and put in the queue to be fixed. http://www.apple.com/feedback/macosx.html
2. Here might be another for you.
Do you have any Flagged emails?
Yes, I use Flags extensively.
If so, are there any that are Unread?
I have 133 flagged emails and the Mail program says that all are Unread even though they have all been read and do not have the blue dot next to them.
I can even add a new flagged email and it says it is unread even though I just read it.

I didn't have the unread issue, but I did have some flags reset to red. Total PITB to reset correctly.
If the flags are set properly, you can create folders inder "On My Mac" (red flags, blue flags etc). Copy not move the messages into folders. This will give you a backup in case resetting FlagMailboxes.plist looses your assigned flags.
Let me know if this helps with your flag unread issue.
