I have found that quicksaving prior to initiating the landing sequence and then load the quicksave will get it to do the deorbit, course correction and braking burns right. Why this works, i've no clue. However, it still goes toes up right after it kills the last of the vertical velocity and is supposed to assume a 90/90 heading for final decent. Instead it starts twirling about like jeb lost his mind or something. Aborting and hitting land somewhere doesn't seem to help. I've had to do the final manually or with the help of smart ass holding the 90/90 heading.