This sounds like incoming.pl crashing when being ran. If incoming.pl crashes it will not
send QUIT to the POP server so no messages that were marked for deletion will get
deleted. Are you running in shared mode? Could you run incoming.pl in telnet with
-v flag for debugging see what is happening (be sure to take it out of cron before
you run it manually, some POP boxes lock the account when one connection is active).
If you are not running in shared mode, could you turn debug on in the admin and tail
your httpd error log when you check your email and see what is happening?