You might be going about this the wrong way, from the sounds of it.
Whatever IS going on, is perfectly right. Change is a good thing – it simply might not be a good thing for your relationship, and that's OK too.
That's probably why she gets self-conscious, angry and offended as she sees you thinking there is something wrong which simply isn't the case. Stop questioning and start showing empathy and interest in her. Encourage her growth and maybe she'll open up and share with you. That's never going to happen when she thinks that you think she's broken – that's how mental blocks form.