I had a similar experience a couple of years ago. She complained I was never in the office at 4:30pm, when I might have been needed. I countered by saying I never saw her between 7am (my usual start time) and 9am (her usual start time).
She accused me of sabotaging a project, when in fact her consultant had cocked it up, and blamed me. I later had to retrieve the situation.
During a reorganisation, I was one of four chasing three jobs. Despite lots more experience, performing well in interview, presentation and external testing, I missed out.
When I spoke to HR for feedback, they told me I scored 100% in the test. Someone had sent me a list with my name on it with 'Headcount Reduction' entered beside it. The other three people did not have this. I showed this to HR and complained the process was rigged against me. They were livid. I threatened legal action. They ended up giving me a cushy job for two years, and in a month I will leave with a redundancy payout. It really couldn't have worked out any better.
My advice would be to gather up as much evidence as possible against her, that she is treating you unfairly, then talk to your HR department.