Atomicorp

Do you have to run qmail-scanner-reconfigure? Seems the changes to the file don't always stick..

I'm upping my $spamc_binary='/usr/bin/spamc -t from 30 to 350 and it seems that it reverts back to 30...

Every time you run qmail-scanner-reconfigure, the qmail-scanner-queue.pl file gets rebuilt with the new options. To change the timeout, you need to change it in:
#/usr/share/qmail-scanner/configure

Then when you run "qmail-scanner-reconfigure", you change will be there.