Found a workaround:

Under 'Preferences -> MIDI Driver' I had always my master-keyboard as 'Input Driver' and Microsoft GS Wavetable Synth as 'Output Driver'.
When I unselect the latter and chose '<No MIDI/sound output>' the problem is gone.

It's still a bug, but at least I have a workaround now...it was a bit tiring to regenerate each track by hand each time...