When I create a node using MJ and then try and fine tune it with Node Editor the node jumps to show a completely different result. This seems to be because the Numbers getting put into the Node Editor are incorrect. Mostly it seems to be a pos/neg flip.

For example I do a match target plane node then true to edit it to line up for an intercept and the projected orbit goes way off where it was. The Normal value in this case seems to be flipped so I either add or remove "-" before making changes in node editor.

Seconded. I was just doing an Eve transfer with an inclination change of around -360m/s Normal+. Every time I went back to that maneuver node it would remove the negative.