I'm sorry to hear that Christopher! This might mean that the largest_content_change_number in the user's folders.json file is out of sorts.
If you check this value for Inbox in a copy of one of these user's folders.json do you see that this value is significantly higher than the content_change_number value for the same folder (Inbox)? I recommend checking a copy of the file to avoid locking the original which can lead to problems in SmarterMail.
Ultimately I think this one might warrant a support ticket, so please let me know when you submit that and I can grab it and we can pick up where we left off. Thanks Christopher!
Kyle Kerst
IT Coordinator
SmarterTools Inc.
www.smartertools.com