Glad you got checked out. I was really thinking about posting a question about whether or not you were sure it was muscle pain. An alternate possibility could be something as 'out there' as kidney pain associated with a stone caught in the ureter exacerbated by that particular position or something weird.

On that thought, perhaps on the trainer you stay in one position much longer than you ordinarily would on the road. If, on the road, you're always meandering from drops to hoods to the top of the bars, or stopping and starting at lights/stopsigns or something, the trainer COULD be the big change you're looking at.