> As you can see, it is looking at /var/qmail/users/cdb, BUT with the broken
> box, it doesn't seem to find anything, and just looks at /vpasswd.cdb .

The broken box can find /var/qmail/users/cdb

> Obviously it should be in
> /var/lib/vpopmail/domains/test41.com/vpasswd.cdb, which the Working box
> has found.
>
> Now my question is... is it possible to REGENERATE the
> /var/qmail/users/cdb file? Maybe the problem lies there?

/var/qmail/bin/qmail-newu does this

> From my understanding, the cdb file contains the information on where
> each domain's files are, and since the Broken box can't find it, it
assumes its
> in / .
>
> Is this thinking right? Can the cdb file even BE regenerated?

- Remove /var/qmail/users/assign and cdb
- Remove all test domains from:
  /var/lib/vpopmail/domains
  /var/qmail/control/rcpthosts
  /var/qmail/control/virtualdomains

And try again.

Are you absolutely sure that

vpopmail:x:64020:64020:Vpopmail user,,,:/var/lib/vpopmail:/bin/bash

is EXACTLY the same on both boxes? 64020 sounds like too large of a uid to
me.

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