Problem still happening in 2025.
In short, it is only when using midi over USB.
PRO 3 with local control off and used as a controller for Logic connected to a Mac Mini M2 Pro, Sonoma 14.4.1.
Initially, everything is fine. At some point, while playing, the data sent out from the Pro 3 usb gets note-on and note-off swapped and stays like that (the swapped data is visible on Logic's midi monitor).
Unplugging the usb cable and plugging it back again immediately solves the problem, no need to quit and relaunch Logic or power-cycle the Pro 3.
This happens fairly regularly, at least once a day, but not straight away so it is hard to reproduce.
I need to do more testing but I have a feeling it may be triggered by having a mix of aftertouch being sent out while pressing a bunch of keys.