You can see your quota settings with:
sudo serveradmin settings mail | grep quota
Would you prefer to completely disable quota warnings?
sudo serveradmin settings mail:imap:enable_quota_warnings = no
If this doesn't resolve it, look in your system.log, do you see any quota related messages?
You may want to download mailbfr, then:
sudo serveradmin stop mail
sudo mailbfr -o
sudo mailbfr -q
sudo serveradmin start mail
* the steps above repair permissions and can fix some issues related to quotas
FYI: the original post was from my old Apple ID this is from my current one...
While I have already used mailfbr on the server a couple times, your other recommendations appear to be more appropriate to this issue. I hven't tried them yet because I am also in the process of upgrading the server anyway. However, I will try your recommendations after thie current active server is demoted to the backup role.