Another weird little clue just occured. I'm starting to think there may be more than one cause of Sonar messing with plugin settings.
What happened was that I had a synth part running on loop in quite a large project. I then inserted an instance of Pro-Q onto the track, as the transport was running, and activated a high pass filter at 200Hz. Inserting plugins during a looped playback sometimes causes MIDI to go out of sync in large projects for me, and it did this time. So I stopped playback with the spacebar, and immediately hit space again to restart from the start of the loop. At the exact same time I did this, the high pass filter in Pro-Q jumped down to 30Hz in front of my eyes, without me touching it. I did the same actions again with the same results. I'll try and capture it in a screencast. I tried reproducing this in a fresh project but of course it didn't happen - so there must be some combination of conditions, which aren't present in a fresh project, which causes this nonsense to happen.
I remain quite sure that certain actions cause Sonar to send errant automation data to plugins, and stopping or starting the transport seems to be one of them. Someone else reported that they saw the Quadcurve settings being messed with as they clicked the cursor back and forth to different locations in the clips pane. And finally there's this which I've posted before - evidence of Waves Q10 settings being messed with when turning the ProChannel on: