Are you canting the bow? If so, are you canting alot? I ask because you may be seeing tail left that shows up as high if you are canting a bunch. If you are canting try shooting the bow vertical and see if your results are the same.
If this isn't the problem it sounds like you are getting contact with something. Maybe the fletching is bouncing off the shelf??? Could be caused by the alignment of your nock or you could even be exerting downward pressure on the arrow that makes it contact the shelf.
One last thing, you certainly can try adjusting the brace height. I can't think of why that would be causing your flight problems, but it is quick and easy to try. Good luck and keep us posted...Mike