Today this bug also accured in my game and I can confirm what you said, Simon.
I have mounted a Probodobodyne OCTO on top of a Mk1 Lander Can in the same Stage. This was the first time I used the Lander Can instead of the Mk1 Command Pod, so I switched back to the Command Pod. This didnt change anything, what lead me to this forum.
So I tried what you said and it seems that dividing the two control parts either by a decoupler or docking ports solves the issue.
Edit: Well, seems like it isn't that easy. I tested what I wrote above only on the launch pad. Now I completely removed the remote control, flew to Minmus and tried again to take some surface samples. As soon as Jeb climbed back into his Command Pod the bug occured again.
