This has happened to me, except I don't even see a Ap or Pe indicator when this happens. I'm on v0.1.4.1, no mods.
Nothing seems to fix this for my craft that is currently affected. I've tried going to the KSC, then back to the tracking station to take then control of my craft. I've tried saving and exiting out of the game entirely. And just going to tracking station and then back to craft.
I did some investigation and found some interesting things:
My save opens up straight to th