Sorry about the trouble getting things working with The NDLR. I know it can be frustrating to get a new piece of gear integrated, and it doesn't help to have things changing unexpectedly. Do you have anything plugged into The NDLR's MIDI inputs or could it be receiving MIDI on USB? It sounds a lot like its getting CC messages that could change its parameters. When you restart The NDLR whatever changes were received would be gone. There's no way to disable The NDLR control channel, but make sure its not set to the same channel as KB Trans (settings menu 1).
The motif pattern setting Patt Note Type: chromatic-fixed is what would cause the motif to not change with the chord. If it happens again, before restarting The NDLR, check the Pattern editor screen to see if the motif was set to chromatic. If its changed, that's a sure sign The NDLR is receiving data from something.
There no case in which The NDLR will leave notes on. We've monitored the output extensively and have never seen a case where there isn't a note off following a note on. However, the time between note off and the next note on is very short. Its MIDI spec compliant, but some synths can't handle it. The latest FW on the Open Beta FW forum adds a short delay between note off and the next note on. This might help with stuck notes on a problematic synth. In any case, you should try updating to that firmware if you haven't got the latest already.
The motif pattern setting Patt Note Type: chromatic-fixed is what would cause the motif to not change with the chord. If it happens again, before restarting The NDLR, check the Pattern editor screen to see if the motif was set to chromatic. If its changed, that's a sure sign The NDLR is receiving data from something.
There no case in which The NDLR will leave notes on. We've monitored the output extensively and have never seen a case where there isn't a note off following a note on. However, the time between note off and the next note on is very short. Its MIDI spec compliant, but some synths can't handle it. The latest FW on the Open Beta FW forum adds a short delay between note off and the next note on. This might help with stuck notes on a problematic synth. In any case, you should try updating to that firmware if you haven't got the latest already.