Hey Joe,
I'm not exactly sure what hardware you are using, but I am going to assume that when you mention the USB port you are talking about using a USB to RS232 converter. My first questions would be what is the model converter are you using.
I know the NI USB-232 converters work flawlessly and are designed so that they show up as a native serial port under Windows as an additional serial port and fully support all of the same commands.
Be aware of cheap converters that may not fully support all of the functionality found in built-in serial ports or ones that use cheap drivers. These cheap converters may not be compatible with VISA or your hardware.
As a test I would recommend opening up the Windows Device Manager and first make sure that the add
itional serial ports show up. Next, open one of the Windows applications like hyper terminal to see if it is able to communicate with your hardware. If this fails I would recommend using a different USB to RS232 converter or contact the manufacturer for assistance. Let us know if you are using an NI USB-232, what OS you are using, or if you are connecting the USB port directly to your device without using any RS232.
-Josh