Those are pretty strange. I mean, the scratches might have been quite bad before you got her and maybe that is scar tissue underneath? I would have thought the vet would have mentioned that. I cannot think of anything that it might be except scar tissue since you mention the vet said they might not go away, but then, if more knots came upon riding her, that would make me think of fluid. . . Are they hard or moveable? Maybe there is fluid that needs drained? I cannot imagine it being something that cannot be corrected - it seems strange, but simple - for a vet, at any rate. If the vet wasn't more clear, I'd probably call another out for a second opinion. Do they seem to both her at all?
On another note, I'd say she just has high withers. I don't think she appears swayed backed at all.
Best of Luck!