OK. I was having the same problem as Iain. If we su to vpopmail and call qmail-inject (via mutt) the message gets sent through to the aliases correctly. Seems that this is a problem with the way that maildrop passes permissions to vpopmail.
If we call qmail inject without a mailfilter file, then vdelivermail is invoked as user vpopmail. If we call it with a mailfilter, it is invoked as the user that invoked qmail-inject. Ideas? Todd Ellison