Middle D is always the hardest key to play with a tone similar to middle C. You can play middle perfectly in tune with a tuner, but the tonal sound is hard to match with the tonal sound of middle c, so it sounds as if its out of tune, when it isn’t. With more experience your embouchure will improve to make it sound better.

If you dont understand what i am talking about, play a normal Bb and then compare the sound to the alternative Bb fingering positions, they all tonaly sound slightly different