When I first got my 919, I did the same thing at one particular spot on my ride home every day. I would make a left from a yield, run up the RPM's, and shift while coming out of the turn. Never failed, I didn't pull up far enough and the bike wouldn't shift all the way into second. I switch to a GP setup, and I make sure use solid, clean movements every time I shift.
You could also try to move the shifter down to force yourself to lower your toe a little. That makes it easier to make sure you have pulled all the way up on the shifter.