I had the same problem, and yes it's really makes the game unplayable. I was building a space staion, so I launched a hub first, which has no engine at all. But when I control the second part to dock with it, the hub just suddenly change to a crash orbit. I'm pretty sure the orbit is high enough, the PE is 69160m, away from the atmosphere. I upload two screenshots, one is before the change of the orbit, the other is after.