Unfortunately I haven't done any testing on Windows 2008 or Exchange 2007 with POP Collector as yet. With Windows 2003, POP Collector runs as a service but is configured via the UI. When you open POP Collector, it automatically checks to see if the service is running and stops it. You then have the UI so can configure while it is running. Once you close the UI, the service is automatically restarted.
It may well be that the above does not work in Windows 2008 - though I will test on this soon (I do have access to a 64 bit server on which I can do this, it is just the time that is lacking for this at the moment!).
From the UI, you can force POP Collector to do an immediate download (there is a Collect Now button). But you do of course need to get the UI up.
It should be that even if POP Collector on Windows 2008 doesn't detect and close a related service, the UI should still work - so if you were expecting an email you could fire up the UI and Collect Now.
Of course, the best solution (and I hate to say this

) would be to configure the mail system to not need POP Collector - i.e. mail comes directly into Exchange. This way, mail is delivered immediately anyway. I tend to use POP Collector as a backup email system now. The server receives mail directly, but the backup MX is set to the ISP. POP Collector is then configured to check the ISP account periodically in case of connection issues that caused the backup MX to be used for delivery.