I agree with smrobs - I wonder if perhaps her neck is sore or tight in a way that makes her mane being pulled on uncomfortable.
I know my mare has a really tight neck and, while she'd always "tolerate" me messing with her mane, since she started getting regular massages -and the loosening of her neck that came with it- she's been a lot more "whatever" about her mane.
If I remember correctly, your girl is an Arab cross? My theory is that having a tight neck is a pretty typical Arab "thing" - due to how many of them bomb around with their necks all up in the air.
At least, my mare with a tight neck is an Arab and another horse I worked with that had a super tight neck was an Arab cross.
...but 2 or 3 does not mean it's a proven fact.