Drivers in Windows provide 'virtual' COM ports. You configure the driver to provide COM17 or whatever, and then pick that in your software.
The usual problems are if the software is badly written and only allows a limited selection of ports (only allows COM1-4 or COM1-9), but if you don't need to drive lots of other ports at the same time you can just configure the driver to be COM3 and there's no problem.
If the program won't work on 2000 or XP you might be running into the 'needs hardware access to port' issue that others have mentioned. (Likely if they're bit-banging the control lines and not actually using it for RS232). USB won't work for that.
Theo