Com1 isn’t working

I have a DOS application in Windows 2000 Pro that uses a modem to transmit data. The problem I’m having is that on the DOS application it only uses COM1 and COM2 for the modem. But when I install the modem it goes to COM3. I try to assign it to go to COM1 but it says that it’s in use. But I don’t have anything using COM1. When I force it to go to COM1 works fine but after I reboot the PC it stops working. It will says no such file COM1 exists. Can any one help me?