Weird user/email quota issue - maxes out no matter what you set

Having a weird issue with the Quotas in virtualmin.
Random users everyday are getting their quotas maxed out even when their mailboxes/home folder are empty.
If you increase the quota Eg, Doubling it, the amount of quota used, will max out again in a few minutes for that user.
Rebooting the server clears the quota issue for affected users, but other random users will have their quota maxed if you wait long enough. Users with maxed out quota have mail issues, but if set them to Unlimited, then everything functions again. I did a search for files for the user and there does not appear to be any files taking up space owned by the user that would account for the space.

Does anyone have any suggestions where I should start looking to troubleshoot this issue?
It sounds like the quota script may be having some issues?

It is VirtualMin 3.82.gpl on Debian Linux 4.