I did delete a few files from the queue using qmHandle, but not many.

What program is qmHandle?  Apparently, it messed up your queue.
   
   I ran ./instcheck /var/qmail and it just hangs...

A bad sign.  Could you copy here the check: and instcheck: stanzas from
the qmail Makefile?  I just cannot remember how they were in
qmail-1.01.

   >     echo Starting Qmail
   >                    nice -20 env - PATH="/var/qmail/bin:$PATH" qmail-start
   >    ./Mailbox
   >     splogger qmail &

You are delivering to users' Mailboxes (using qmail-local then) but
then you have links in /usr/mail?  It is also possible you made the
links in the wrong direction.  You need to have links

/usr/mail/joe -> ~joe/Mailbox

not the other way around.

Mate
---
Mate Wierdl | Dept. of Math. Sciences | University of Memphis  

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