Hi,
The issue I encounter is related to how mail.app handle EWS operations for an Exchange 2010 account (no issues for my two others Exchange (cloud) accounts whatsoever). I can send mails, change items indicators (read, unread, flag, ...) and it syncs properly, but mail doesn't refresh folders on synchronization. I have to reopen the app to sync properly (even connection reset doesn't do the trick).
I checked server-side and I managed to see sync requests goes by without issue. I wanted to check logs client-side, but they are empty. I spoke to AppleCare Outreach about the issue, but they cannot give me a feedback. It was 2 or 3 weeks for now and I didn't took the time to open a case. If you have the same issue, it's not yours to solve.
That being said, I spoke a bit too fast this morning; I saw that the update would solve an Exchange connection issue in mail.app and immediatly applied it yesterday, then recreated the faulty account (didn't worked before) and it worked again as intended ! But since I rebooted (yes, rebooted, because of a non related issue) my MBA this morning, the issue came back. I don't have time right now to test everything on different configuration, recreate again the account and so on... I'll try asap and write back here if I find something.
Hope it helps to pinpoint the issue.