We have had a similar issue here three times:
1. The first time this occurred the issue was exactly as you described for #1. Due to a corrupt root file for the users Mailbox. I had to open a support ticket to have this resolved. There was some back-and-forth over 'size' of the ActiveSync account, but it was really due to finicky support by ActiveSync for special characters and the inability of SmarterMail to resolve those. Why this only worked occasionally is probably due to the way that ActiveSync was delivering items.
2. A user was having synchronization issues which was related to an Outlook plugin by QuickBooks/Quicken, this prevented mail from Synchronizing at some points, just sitting as if it were not receiving mail.
3. We currently are opening a support ticket for one user who occasionally has problems with synchronization where the users iPAD and iPHONE will receive messages without problem, but the Outlook (2013) clients will halt at various points. Sometimes reconfiguring the account will work, we did track one down to what appeared to be a corrupt event, but the users mail ceased a week later despite that. We do not have this problem with all users, or even our heaviest users.
Hopefully SmarterMail monitors these threads occasionally