I experienced strange behavior of the landing autopilot. Well not exactly the autopilot itself, but it affects it. For some reason sometimes (not very often, but it happens) the landing autopilot does the deorbit burn, but stops at course correction
I know what you mean but not sure this a mechjeb issue.
In my case my craft had enough power but mechjeb displayed 0 power. By manually transfering power (alt rightclick battery/module-->alt rightclick mechjeb and transfer) I got mechjeb working again.