I have a USR 56K external USB modem on Win98SE. I'd get this occasionally, especially after a restart or cold boot of the computer (the message would say "Port already open"). This was the fix:
1) Turn off the modem and go to Control Panel>Modems and delete the modem.
2) Restart, then turn the modem back on, Winderz would find it and that was that.
In order to keep this from happening again, when I reboot, I go to Control Panel>Modems>Diagnostics and select the modem and click "More Info". It then returns the string of AT settings and other gobbledygook and I'm good to go. I just make a habit of this whenever I restart the two machines with these modems.
If yours is an internal, you can skip the power off-power on thing for the modem (obviously) but the rest of it is worth a try.
P.S. This was the only thing I ever got that was helpful from the MS phone tech support. I just happened to get a guy who had the same setup and he clued me to it.