How did you even try to program that? MSC400 + MX3000 could only be programmed in CCS. There's no way you can add a MX6000 to that setup without importing the file into CCP, converting it's format to CCP and dragging all of your hot key commands to the MX6000.

If you're programming IR into the MX6000 and trying to pass it through the MSC as though it was a MRF260 or 350 you need to make sure you have the output for that device set to RF in the MX6000 program.

I think the main problem you have is two different configuration files with some old and new hardware.