A long shot, but here's how I experienced similar symptoms: http://www.dovecot.org/list/dovecot/2016-April/104091.html
Kamil Madac wrote on 08/23/2016 02:02 PM:
Hi, One of my email accounts has 1,5gb of emails in INBOX, but maildirsize shows only 528mb. 'du' also shows 1,5gb and there are 3809 files in cur directory. When I use mailbox status a can see correct values: doveadm -f table mailbox status -u u...@domain.sk "messages vsize" INBOX* messages vsize INBOX 3809 1521049349 but when I check the quotas with doveadm: doveadm quota get -u u...@domain.sk Quota name Type Value Limit % User quota STORAGE 541391 2048000 26 User quota MESSAGE 886 - 0 I tried to delete maildirsize, but it was recalculated again incorrectly. 2097152000S 554384829 886 Dovecot version is 2.2.9 installed from packages on Ubuntu 14.04 I have other accounts on server which are have no problems with maildirsize and quotas. Does anyone have same experience? Kamil