That is odd considering MCC should change the channel settings on your BSP immediately, without need for you to transfer them across.
What about if you set the channel from the front face?
Select a track and press and hold the CHAN button. There it will display which channel each of the tracks are set to on by lighting up the step buttons with colours corresponding to the tracks, with red being the USER channel. While you do this you can change the channel the currently selected track is set to by pressing a different step button. Do this for the 2 SEQs and DRUM tracks, as well as Control Mode to set the USER channel.
Now although it should happen automatically when you connect your BSP to MCC, just check that you have the current firmware loaded on your BSP. Back-up your projects, update the firmware then do a factory reset, then transfer your Projects back onto the BSP.