I don't fully understand the intricacies here, but I assume you're using Exim or Postfix which allows you to pipe an email address/alias to a command.

It's stabbing in the dark a little, but you may want to check permissions - often Exim will try and execute such an external script as the user Exim is running as (which should be a non-privileged user) so it may not have read/write access to the files you're expecting it to have

Also, it's possible that the MTA is expecting some sort of feedback from the script after it hands the mail over

Sorry I can't offer anything more concrete, but perhaps if you could post some more details about your Perl and its plugin to your MTA that might help.

--Alex