I have only seen that happen once on my setup. It's when I was looping the capture in the focus module (I thought I had the imaging camera selected, but it was in fact doing the guide camera instead)
Make sure the guide camera is only being used in the guide module.
Another time I had issues is when I was capturing dark frames for my guide camera, the system would allow the guide camera to capture guide stars, or focus even though it was doing a dark capture (it messed up my dark capture session).