Hi Chris,
Been checking through my Microsoft books and on the support.microsoft.com web site trying to see if I can find a way to configure a COM port programatically, not having much luck.
I found some references that suggest that you can add extra parameters to the RUNDLL32 command line, but I can't find anything specific showing how.
The other thought is that with Plug and Play technology, all you'd have to do is reboot and the modem would configure itself when the OS detects it. Of course, unless you just wanted default values for the baud rate and such, I don't know if that's a good solution or not.
I would suggest checking out the Microsoft support web site, or perhaps their support newsgroups, I'm sure someone up there would have specifics on how to do this.