This sounds remarkably similar to a problem I’m starting to have. I notice the same behaviour but when automating the ‘mute’ function on the track. No plugins involved, just the simple ‘on/off’ track mute automation lane (in this case on a group track). And, like you, I can’t seem to recreate it in a reliable way yet, but it’s happening regularly. Cubase seems to ignore some of the instructions but not others, and each playthrough it’ll choose different ones to ignore. Reloading the project solves the problem, so this sounds more and more like a bug to me. It is worrying, I use lots of automation in a mix and need to know it’s reliable.
Details of my problem can be found here if needed: