Sorry, I completely miss that you need full output log. Here it is (warning! 145 Mb size, it's from my attempts to turn-on and turn-off hibernation).
I can provide save file too, but my game heavily modded (something like this) so I'm unsure in results.
Here, my save file where I cleared all probes/relays/debris/etc, so remains my only 2 piloted vessels. One of them landed on Minmus. When I try to fly it with enabled hibernation - I always receiving endless warnings and massive slowdown. That vessel shouldn't use any modded part (or at least I don't find them).