The cruise M has a bug that shows itself occasionally. It seems to happen when the track power is ramped up from a chopped wave transformer. The radio board ends up in command mode and the Cruise M ends up in conventional mode.
You might try this. With the engine on the track, advance the power to full. Then take the direction button on the transformer and hold it down for ten seconds, then release it. Note: not the direction button on the remote. It must the the direction button on the transformer. If the radio board and the CCM boot up at the same time with a full sinusoidal waveform, it usually runs OK.
If your control system uses a TPC, then boot the loco up with AUX1, 9. That will put out a sinusoidal waveform.