Hi Euripides,
It sounds like the Ground Control is sending MIDI CC messages which are triggering the Repeat and Tempo changes on the TimeFactor. in the RCV CTL menu of the TimeFactor's MIDI section in System Mode you can de-assign things from being controlled this way.
I would check the settings on the Ground Control to make sure that it is sending MIDI Program Change messages, which are needed to change Presets on the TimeFactor via MIDI.
