Try the Minimalistic MIDI profile or watch the recent MIDI event window and see if anything stands out as causing the tuning change.  You can also, in a preset, turn off MIDI events for particular sliders and settings, if you determine which is the only sending it flat.  Often, if settings in Pianoteq aren't visibly changing or you're in Stage, it makes it more likely that it's the pitch bend event getting activated by something.