Same Issue here, and this was before the November update. No matter the selected input transpose channel or the input mode - USB/MIDI. The only future that works is the latch on/off mode.
This issue is tricky. It is now always present. Sometimes, when the transpose channel is set to 2, I can transpose it with a NI Maschine and internal Midi routing to the BSP, and in that case I can hear the incoming notes only when the REC is blue, otherwise it transposes. The other midi keyboard, connected to the midi in in the BSP plays and recs normally. Curiously why the 2 channel are not behaving normally thought.
I wii try to reproduce the issue and make a screen video on it.