Some devices (cards) have a specific com port that they work on. Unless you have a server computer, I bet you don't have more than a maximum of 3 com ports (1,2,3). A lot of motherboards I have installed in the last year only have Com Ports 1 & 2. Notice, that if you go into System Resources, you will see that certain IRQ's are directly assigned to Com Ports 1 & 2.
First of all, go into BIOS and make sure that the BIOS is set so that Com Port 1 & 2 is assigned a fixed and definite IRQ, ok?
If you have been messing around with the BIOS and have assigned IRQ's to other things than the Com Ports, this could well cause the problem, as BIOS will dictate where resources are assigned over the operating system.
Alright, so you have gone into BIOS and made sure that an IRQ is assigned to these two Com Ports. If the problem persisits, you may have to change resources, by selecting a different set of Hexidecimal values in the BIOS. Notice that the IRQ's can be set to alternate values (I would give them to you, but I am not at my BIOS level right now). If the modem does not recognize Com 1, 2, or 3, then change the hexidecimal resource value in BIOS and then try again. Make sure you write down the original settings before changing them. Changing them won't hurt anything, it may end up freeing the resource.
It may end up doing nothing in which case you have not lost anything...just set the original hex resources back per what you have written down.
Alright, now, the other problem involved with not recognizing the Com Port is that usually, the modem and the sound card end up fighting each other for resources (IRQ's). A lot of modems will try IRQ 5, 9 or 11. Go into Device Manager and see where your Modem is installed and what IRQ it is using. You can troubleshoot using System Information and taking a look at any resource conflicts. It may well be that your sound card or maybe a network card is taking precedence over the modem on the PCI bus.
You may have to delete out the modem driver(s) entirely and then reinstall them again, in order to clear the IRQ resource sharing. This will help to re-arrange the IRQ settings. Your sound card or network card may be hogging more IRQ's than it should. By removing the driver(s) for the modem, Windows will be able to re-assign IRQ's. I am of course assuming that you have a PCI modem which is capable of sharing resources with another device.
After doing this, reboot and try to reinstall the drivers. If this still does not work, you are going to have to uninstall and reinstall your sound card/network card.
This means, you are going to have to delete those drivers out, in Device Manager, get out and pull the cards out (sound and network) and then just install the modem alone. This will definitely free up system resources making the modem your sole PCI card. This should clear up the problem with the COM port too.
I would recommend that you try a different PCI slot, maybe PCI Slot #2. This is normally where I have the best results with a modem. Do not use PCI Slot #1 because recent motherboards have sharing conflicts with the AGP Slot. Use #2. Then, after you have done this, move on...re-install the sound card, by skipping a slot and put it into PCI Slot #4. Get the sound card up and running again.
Finally, if you have a network or other card, try to use PCI Slot #5 first. If this does not work, try PCI Slot #3.
I find that this usually takes care of a Com Port problem.
I know, its a lot of unexpected work, but deciphering why the modem is looking for a Com port that does not exist (like Com Port 5 on a 3 port Motherboard) is beyond the scope of this discussion.
I am, of course, assuming you have, 5 PCI slots on your motherboard.
I hope these suggestions help and solve the problem