Xenorollmops

You are not alone. I have similar issues. During transition from 100km Kerbin orbit to Jool, all of sudden, steering locks up and the "magic" starts to happen. After throttling down AND EVEN staging, thereby ditching the current engines, acceleration continues. In addition, the camera focus of the craft is totally messed up as well. The craft is focused on a few 100m in the distance, if ever. Switching the camera angle, leaving to map or KSC does not change the behavior.