I didn't realize she was boarding at the trainer's. She might simply be nervous at being in a new place with people she doesn't know. It does sound like she has a real strong emotional attachment to you, so yeah, it might be as simple as scared and confused without her "mommy"

Admittedly, I've known horses that would milk any emotional coddling they got for all it was worth -- and then I've known horses that really needed that emotional support to feel confident and secure. Hopefully your trainer is sensitive enough to spot the difference, but I always worry when a trainer seems honestly to dislike a horse, ya know?