One guess: your mail_location is misconfigured.
something like:
mail_location = maildir:/usr/local/%u/Maildir
might fix it up... 
-- 
Computerisms
Bob Miller      
867-334-7117 / 867-633-3760
http://computerisms.ca
On Fri, 2013-08-16 at 17:09 -0600, LuKreme wrote:> My virtual users have their mail stored in /usr/local/virtual/user at
example.com/
> 
> dovecot wants to read the mail from /usr/local/virtual/user at
example.com/Maildir which is causing problems since all new mail is being
written in /usr/local/virtual/user at example.com/new and dovecot is looking in
/usr/local/virtual/user at example.com/Maildir/new
> 
> For the local users, /home/user/Maildir is the right directory.
> 
> for right now I've had to kludge a script that moves mail from 
/usr/local/virtual/user at example.com/new to /usr/local/virtual/user at
example.com/Maildir/new every two minutes.
>