How long have you left the boots on for her to "get used" to them? Have you worked her for a good hour in them to really give her a long chance to get used to them?
Have you done any desensitizing work with her, especially the back legs? This could help.
And completely silly question, but make sure you have the left boot on the left leg, and the right boot on the right leg. I've seen people at shows walking around with the wrong boots on the wrong legs, so that's why I mention it!
Does she have any residual pain from that tendon injury? Maybe the boots somehow remind her of that incident?
It might be very possible she just may not tolerate the boots. She an individual. She might just not like it. If that turns out to be the case, just use polos on the back (provided you know how to wrap them properly. If not, have a vet show you.) Lots of barrel racers run with boots on the front legs and polos on the back. I myself prefer boots on all 4 legs, but if she won't tolerate them on the back, you can't force her.
∞•*˚ Βгįťţαňγ ˚*•∞
It is not enough to know how to ride; one must know how to fall.