The best thing I ever did was to buy a copy of the Employers Handbook Guide...
Even as an employee (now an owner) this book has saved me from a managers stupid, wrong, or wierd emotionally driven desicions countless times.
I'm glad to hear it worked out in the end... but you should get to know your employee rights.
For example: in most states you can only be fired on the spot for; stealing or drug use.
(I'm on your side here ) She should have talked to you about not clocking out and told you it was a major issue for her. But, Not clocking out can be construded as stealing if you are trying to get more hours on your paycheck.
Still, your manager should have followed standard procedures to avoid potential legal action by giving you a verbal warning, a written, then a final terminal warning/firing.
Or in simpler terms she was wrong and that's why the regional manager overruled her.
I suggest you buy the book I mentioned or keep notes on your manager's weird decions with the time and date to establish her pattern ONLY TO BE USED if you get "fired" again...
most lawyers won't take a wrongful termination case unless it's clearly a bogus firing with notes, witnesses.