OK, Maildir is the right storage format for large accounts. Please hae a look in your mail log and syslog if there are any errors for this email account. If you search for a specific user in the logs, you can use this comand:
tail -n 1000 /path/to/the/logfile | grep "webX_username"
This searches for the string "webX_username" in the last 1000 lines of the logfile /path/to/the/logfile.