I'm experiencing the same problem. It seems like a bug to me.
no matter what channel I set in the MCC for transpose, or the ports - it's transposing the sequencers when I don't want to.
EG: MIDI keyboard playing via USB on Channel 1
Sequencer 1 is set to accept MIDI channel 1.
Transpose in MCC is set to "MIDI port only" and to receive on Channel 13 (which is unused)
I can record notes just fine, etc. into Seq 1, but if I Seq 1 is playing and I touch my master midi controler, and play on Channel 1,2,3,4,5,6,7,8 ... it will transpose Sequencer 1 and Sequencer 2.
To be clear: Pattern Transpose is recieving on all ports and all channels and no combination of MCC setting is deactivating this