Show us the output of:
/var/qmail/bin/qmail-getpw root
Also as root:
# su - alias
$ cat .qmail-root
> >Surely you mean ~alias/.qmail-root?
>
> Yes. Or, more properly, /var/qmail/alias/.qmail-root
Actually, ~alias is "more properly" as it's the home directory
of alias that counts, not that it's in the /var/qmail hierachy. I guess
that begs the obvious question that ~alias has the home of /var/qmail/alias?
> >Do you have any other ~alias/.qmail- files? Do any of them work properly?
>
> As above, .qmail-postmaster. I haven't tested postmaster yet. I'm going
> to presume that it'll fail.
Sounds like it's easy enough to test and would provide useful information.
Since no one yet knows exactly what's happening, presuming is probably
a risky attitude.
Mark.