If qmail-scanner-reconfigure simply "hangs" (i.e. more than 10 minutes for example) and you want to know what it causes, do this:
Open /usr/share/qmail-scanner/qmail-scanner-reconfigure.psa
At the end of the ./configure section comment the line "> /dev/null"
So after editing it should be:
# > /dev/null
save the changes and rerun qmail-scanner-reconfigure
Now the reconfigure offers an output about what it does.
Look for errors and fix it.
Have fun !
Bart