mikysee,
My guess is that you have one Com1 configured in the BIOS and the other Com1 configured on an installed device. Don't forget Com1 is just a generic way of referring to an IRQ and an input/output range.
Com1  IRQ4  Input/Out Range 3F8-3FF
Com2  IRQ3  Input/Out Range 2F8-2FF
Com3  IRQ4  Input/Out Range 3E8-3EF
Com4  IRQ3  Input/Out Range 2E8-2EF
So I would look for a BIOS setting specifying COM1 as being configured (and try to disable it) or pull out all non-essential cards (ie. leave in video card) and reboot to see if it took care of itself.
Another possibility is that Windows sometimes gets confused. Manually removing the fully functional port (ie. the one without the exclamation point) works. On the other hand, manually removing the non-functioning port (ie. the one with the exclamation point) works as well.
I would just play with it and see what happens.