It has to be a confidence or sharpness issue - he's shown he's a competent finisher before. I completely agree there's more in his locker. I just hope we don't sell him in the summer. He hasn't done himself justice here so far and of course he's partly culpable for that, but it is a worry if we can't find a way to accommodate this type of player.
Just out of interest, how did he perform for Dortmund against Bayern @Balu and @Sphaero ?
His last game for Dortmund was against Bayern in the German Cup final if I remember correctly. He was one of the best players on the pitch for Dortmund, and Fergie+Phelan were both there in person on a scouting mission. I think it was reported afterwards that Fergie and Shinji spoke after the game.
I think he should definitely play against Bayern, especially with Mata being Cup tied, and RVP out. It's tailor made for him behind Rooney in the 10 spot. Give him someone with pace and good movement like Welbeck and Nani, with Rooney in front, and it'd be a decent front four.