Hello Antoni,
You could temporarily turn on the "General settings | General preferences | Diagnostics: log all MIDI messages received and sent" setting in Hauptwerk, and OK the screen, and the performance warning(s) whenever they appear.
Then straight after the problem has next occurred (and being careful not to touch anything else first), use "Help | Create a diagnostic file ..." and save it somewhere for reference (in case you need us to look at it).
Hauptwerk's log (which can be viewed using "Help | View activity log", and is also included in the diagnostic file) would then show the specific MIDI event that that Hauptwerk had received to cause the stop change. From that MIDI event you could potentially work out which part of your console had sent those messages and why.
(Note that logging MIDI messages does cause poor performance, though.)