Also, I think you mentioned that you are following a restricted activity plan to keep her from re-injury.
If so, it's very possible she notices that, and is possibly frustrated.
I would continue the restrictions for the planned amount of time. When she regains her freedoms, if this is what's bothering her, she should become well adjusted again.
Her vet did manipulate her arm, which could have increased the pain.:
Is she taking a non-steroidal anti-inflammatory medicine? I forget the name of the one that is widely used for iguanas. My exotics vets used it for post-op pain. If not, I think it would be wise to ask her vet about it.
PS - I think you are doing a good job with her.