Perhaps I am misunderstanding the issue but, does the 990 recognize discrete commands via the USB interface?

Otto, are you trying to do a firmware update or test whether you can communicate using the intended setup for the control utility you are planning on developing?

If you have communications established with the 990 and you know the RS232 commands, you should be able to test things by going to the command line and typing something like:
ECHO [some command] > com2

I personally would not use the USB port on back of the 990 as I am not sure of the implications of sending commands to that port in the "service" mode. Having said that, I am wondering why not just use a plain old serial cable?