Moinmoin,
it is not about the cables, or the MIDI connection as such:
I have MIDI-cables connected (IN, OUT, and THROUGH) in order to sync the P'08 sequencer and modulation (IN) and other equipment (THROUGH) and control a 19"-module (OUT) in my normal setup. I never experienced Your or any other problem with any control tweaked at the P'08. I copy patches - or only one bank of a single patch - a lot, because I often need, use, find, and save new sounds during rehearsals. But I do not really know, if I ever did that while the MIDI sync was in progress, although it might have happened, I just did't care until now.
Maybe Your Logic does something in the background?
Martin