Forewarned: I'm a linux guy without a windows box to look at.
Seems like the problem is accessing from within outlook. If you can filter on the subject line, even Outlook can do that. Use its filters to forward to another email address that can be POPped by perl (Net::POP3). From there, you shouldn't have any trouble.
Can you use the rules wizard to create a couple of rules: one that saves the messages to a folder, and another that triggers a program that then processes it.
I've heard that you can use Win32::OLE to send messages via a MAPI object, but I don't know if it can be used from "within" outlook.