One thing that hasn't been mentioned.. when was the last time she had her eyes checked? DD thought she had excellent eye sight, but I seen some questionable things happen consistently. Took her to the get her eyes examined and found out she had a problem with her depth perception. DD got glasses which was good, but really didn't see the benefits in sports until she got contacts. With your DD's body changing so much, wouldn't hurt to have her eyes checked. I find that's something that always gets overlooked. Especially since you said she's usually an aggressive hitter and she thinks the pitch is much lower than it is.
Don't think its a growth spurt issue. You said she thinks the pitch is below the knees, but you said it's at the knees. I mean it's all relative, her lower (feet to knees) body is growing as well, which means her strike zone has actually become a little higher than when she was shorter and an aggressive hitter. Now if you said that the ump was calling strikes now at the height where her knees were a year ago.. then I would think that would be more of a growth spurt problem.. well actually that would be an umpire problem, .