I don't know if this will help but when I converted to Maildirs
I edited my /var/qmail/rc file to 

#!/bin/sh

#Using splogger to send the log through syslog
#Using qmail-local to deliver messages to ~/Maildir by default

exec env - PATH="/var/qmail/bin:$PATH" \
qmail-start ./Maildir splogger qmail

I think that I read that in some install guide somewhere.
 Having only ./Maildir in /var/qamil/rc would work fine aswell.

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