In case anyone else has this issue, here’s the response I got from Elektron support on this:
I have not seen other reports of this problem, but I found that when “Control 2 (Breath Control) to zero” is checked in Logic Pro Preferences > MIDI > Reset Messages , the velocity parameter of all tracks is set to 1 when double-clicking STOP. Spying on the output from Logic Pro, using a MIDI monitor, I can tell that Logic Pro sends out CC number 4 with a value of zero on all MIDI channels when double-clicking STOP (if “Control 2 (Breath Control) to zero” is checked). CC number 4 will change the Syntakt velocity parameter, which explains the problem. If you uncheck this setting in Logic Pro, it should not happen anymore.