As the owner of 2 arabs, and a total arab lover, here's my 2 cents.
You said yourself that she had been more or less a pet for the past 2 years. Then, when you decide to work with her, the problems started. Without seeing your mare, I would have to say that this sudden change probably confused her. Most arabs are very intelligent, and going from being treated more or less as an equal to being treated as a subservient likely threw her for a loop. She is unable to process this radical change in her life, so she began to act out in order to find her place in the herd again. She likely behaves for Shay-la because she didn't know her as well, and therefore didn't have the confusion that she has with you.
By "laying her down" and using forceful methods with her, you have invoked her fight response. My mare too, is very gentle and sweet, but I know (from my perceptions and her former owner's description) that she will fight you tooth and nail if she percieves that she is being treated unfairly.
Mentally, I believe that you should try and keep the same personality around her as you have for the past 2 years-- don't think of her as a troubled horse. Then I would do under-saddle and groundwork to slowly get her into being a horse again. I would not be aggressive, and would restrain from using force. I am a big proponent of using the "make the right thing easy and the wrong thing hard" approach.
You mentioned that you have an indoor arena-- I would do most of your work in there, so that every time she displays an unfavorable behavior you have the space to put her to work.
Good luck!! It seems that you really want to get to the bottom of this, and my best advise is patience and perseverence without violence :)