I am observing the same issue with the node marker flipping to a different (and incorrect) orientation. After some testing, I noticed it always happens when the flight path changes from an orbit to a hyperbolic trajectory. I am running my games on RSS/RO.
To mitigate the issue, I use MechJeb Smart A.S.S. to lock on the node before the burn. I start the burn normally and before the trajectory goes hyperbolic, I engage the "KILL ROT" mode in Smart A.S.S. so it ignores the node marker.
I hope this information helps to reproduce the issue.
Thank you all for the effort you put into this mod. It is the only reason I am playing KSP again. Excellent work!
