I realise this might be more of a Logic Pro question, but still:
With Komplete Kontrol 3.x, this dialogue appears _every single time_ when Logic Pro gets started. Is there a way to avoid this?
I'm getting this as well with the new S61 mk3. In Logic Pro Settings / Control Surfaces / MIDI Controllers, nothing is showing up in the list, which is probably why this dialog pops up every time Logic starts.
The latest update to Kontakt 7 is what screwed this up. On my laptop, with an M32 connected, it was working fine right up until I applied the Kontakt 7 update. Now the transport controls no longer work. I'm going to contact (kontakt? lol) support.
I found a solution to this dialog popping up every time Logic starts: with Logic running, unplug and plug the device back in again. That should force the popup to display, so click "Auto Assign" again, and then restart Logic. I no longer see the popup on startup and I'm finally seeing the device in the MIDI Controllers section in Logic's preferences.
I also managed to somehow get the transport controls working.