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/u...@example.com/
> 
> dovecot wants to read the mail from 
> /usr/local/virtual/u...@example.com/Maildir which is causing problems since 
> all new mail is being written in /usr/local/virtual/u...@example.com/new and 
> dovecot is looking in /usr/local/virtual/u...@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/u...@example.com/new to 
> /usr/local/virtual/u...@example.com/Maildir/new every two minutes.
> 

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