I would not call this an obnoxious problem. It's very real (to me). 2 thoughts not stated -
1. she took him to his dr appts so he associates her with the dr and pain (shots, whatever)
2. maybe something happened with her that scared him. To be blunt, maybe she did something inappropriate.
Either way, I would respect his boundaries. He needs to know you will protect him and stand up for him no matter what.
What are your instincts telling you? (despite how much you love her)
I do have to say, the way you write it, she's too attached to him. To me, I get weird vibes off of what you wrote. She also shouldn't be trying to bribe him. Play games with him is ok, but constantly bribing w/ toys and food is not a great idea (in my opinion). I'm not sure I believe he's fine when he's alone with her. I would say it's a phase, but it's been going on for over 12 months?
Great book: Protecting the Gift - Gavin DeBecker