I think the commercial suite just give you different room names and some optional modules for lights, etc. It shouldn't matter which suite you use to program, as the back logic is going to be the same. URC isn't going to go through the trouble of rewriting everything. (Look at how you can still buy the MSC-400 new).

Can you do a factory restore of the MX6000 or dump a blank program into it first? Are you trying to DL over wifi or usb?