qmail, vpopmail, courier-imap upgraded from r8 to r9 and every user, new, old, empty maildir was over quota. Rolled back to r8 and problem was solved. Not sure what other info you might want. Needed to get server accepting email again. Reproducible: Didn't try Steps to Reproduce: 1. 2. 3.
Same here
you didn't read the upgrade warning and run the /var/vpopmail/bin/vpopmail-Maildir-dotmaildir-fix.sh script. that is the ONLY change between -r8 and -r9. do the upgrade, then run that script and it all works fine.