This exact same thing happened to me.  The fix for me was to run
/var/qmail/bin/qmail-newu.  This did the trick for me.  Although for me mail
to the main domain worked, just not to virtual domains.  Took me about 4
hours searching through the man pages at http://www.qmail.org/man/

EVERYONE HERE SHOULD HAVE A GOOD MIND NUMBING TOUR!  

Would make Jake's job a lot easier.  :)

Anyway that's my two cents.

NAME
          qmail-newu - prepare address assignments for qmail-lspawn

     SYNOPSIS
          qmail-newu

     DESCRIPTION
          qmail-newu reads the assignments in /var/qmail/users/assign
          and writes them into /var/qmail/users/cdb in a binary format
          suited for quick access by qmail-lspawn.

          If there is a problem with users/assign, qmail-newu
          complains and leaves users/cdb alone.

          qmail-newu ensures that users/cdb is updated atomically, so
          qmail-lspawn never has to wait for qmail-newu to finish.
          However, qmail-newu makes no attempt to protect against two
          simultaneous updates of users/cdb.

          The binary users/cdb format is portable across machines.


  
-----Original Message-----
From: Patrick Ring [mailto:pr...@pringtech.net] 
Sent: Sunday, May 03, 2009 4:27 PM
To: qmailtoaster-list@qmailtoaster.com
Subject: RE: [qmailtoaster] Big problems after old-to-new qmt migrate

Is there a definitive way to tell what version the old server is?
Thank you. 

-----Original Message-----
From: Jake Vickers [mailto:j...@qmailtoaster.com] 
Sent: 2009-05-03 15:05
To: qmailtoaster-list@qmailtoaster.com
Subject: Re: [qmailtoaster] Big problems after old-to-new qmt migrate

Patrick Ring wrote:
> Should it be able to restore a backup done from a very old version on 
> to a fresh loaded version?
>
>   

Depends on how old the old version is. If you look in the restore script
you'll see there's some commands commented out. These were needed when I
went from an old version to a newer one.
The error you said you got about not being able to read a user's dir
sounds like permission problems. Check to make sure 89:89 is free in
your /etc/passwd, since vpopmail will want to use those UID/GIDs. If
your older version did NOT user 89:89, you'll see the qmail-newu command
in the resore script (commented out) as this will be needed to change
the UID for vpopmail. This is mostly guessing though, without seeing the
exact errors/logs.


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Version: 8.0.238 / Virus Database: 270.12.16/2094 - Release Date: 05/03/09
16:51:00


---------------------------------------------------------------------------------
                 Managed Qmailtoaster servers are now available
       Visit http://qmailtoaster.com/QMTManaged.html to order yours today!

Qmailtoaster is sponsored by Vickers Consulting Group 
(www.vickersconsulting.com)

     Please visit qmailtoaster.com for the latest news, updates, and packages.


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