Also can anyone else confirm that the 4.4.4 patch fixes it? I have two IMAP accounts, one syncing OK, one having this issue.
I think there could be a problem when you have the same email address in Mail app using IMAP and in Gmail (but it is not @address, you are logged-in to google using non-gmail email).
On the PC or Galaxy S2 (Android 4.1.2) read status is correct for the same account on the inbox.
I have tried all the suggestions such as resetting the sync days to every different setting, manual sync, turning sync on and off, nothing makes any difference.
Change a message's read/unread status on the server (e.g. Anecdotal reports online seem to indicate that this may be a problem related to imap and possibly specific to SSL, as some people report that disabling SSL is a work-around. t=2748987 I can also reproduce this on my Galaxy Note 3 running AT&T's OTA 4.4.2.