Without knowing more, I would think that it is caused by lopsided muscle development. It's possible that your horse was worked too much to one side and/or the rider is not sitting balanced on the horse.
Thanks iridehorses. I actually had the vet look at it today when he was here for her other million lamenesses (and posted in the other thread about it). He thinks the shoulder that appears hollow is actually normal, and the other is enlarge - possibly from an old fracture.
Pics of her shoulders. The right is the one the vet thought was normal, the other is the bulging one. It was not really noticable when I first got her as she was pretty emaciated. I feel like an idiot for not noticing the huge difference earlier though.
ETA: she is standing perfectly square in the pictures just in case anyone was wondering.
I would look at the saddle fit and also perhaps get an osteo or similar out to look at it as they would be able to look at how the muscle is grown... most horses are a tad unevn in the shoulders but your horse seems a little more so than most :)
We believe its from an injury as I stated above, I was not sure what is was from when I had first posted but had the vet out that day. She was in a horrific accident that I did not know the extent of until today. I had another post about her in this section. She's to be on 6+mos layup and most likely not ridable anymore. And she did have the chiro out weekly for the last couple months.