Long running jobs outside the web port

I'm having trouble with a long running job. I have a protocol form which starts off a long running job in a separate worker protocol. If I run this directly from the PP client, or via a web-link, it times out after 40 seconds (which is the Blocking Job Timeout limit defined in the admin portal), and gives a nasty HTTP 500 error message.

However, if I run this same protocol via the web port, everything's fine. The job runs well beyond the 40 second time-out and completes without any errors (takes about 10 minutes).

My question is this - what magic does the Web Port invoke to make the job immune to the timeout and can I invoke it myself? I don't particularly want to send users to the Webport to run this protocol, and would rather they ran it from a direct link to the protocol form, but at the moment, the Web Port is the only place they can run it without it timing out.

Thanks

Mark