We have the same issue.
Office365 hosted email. Deployed ESET Endpoint Antivirus 6.4.2014.0 via ERA
On 5 or so computers e-mails stopped coming (Updating Inbox or Updating Headers).
Outlook 2013 x86 installed on (Windows 7 x64).
I deleted Outlook profiles, and re-download mail from server. New messages appeared. Still to find out if it will happen again...
If this is related to the deployment please let me know...