Possibility is there. Maybe something similar to a nervous stomach in people. She does have a pretty stressful life....all that transporting. And combined with hard work.
I would feed her like she has it, take it VERY slow with work and see if it has any effect.
I had it resolve itself, just with diet change, in a young OTTB, within about 6 months. Turnout all day, free choice grass hay, a low starch pellet. He smelled BAD, sour kinda, was colicky, tucked up, cribbed, raised he&& at feeding time.....not too happy. It all changed, slowly, but it did.