Sounds very similar to my horse what he used to be like (apart for the being sore to touch in areas). Before I owned him and just rode him In lessons, he came up mysteriously lame is his hind left leg before a little competition in the warmup. There was no indication of soreness when we checked him over, feet were fine, no heat anywhere etc, but he was off completely when in trot and especially canter, we just put it down to he probably knocked it funny during the night etc, he was a little off for a few days then was fine.
After that day I stopped lessons and stopped riding him, didn't see him for a while. He came up for sale in december and we bought him (he is a horse i just clicked with straight away). He was sound, would be fine to ride etc, but he would have his days where he wouldnt track properly in his hind end and would just be off. It wasnt very regular, but he would have days where he would be quite stiff and we thought maybe he is showing signs of arthritis. We then noticed he seemed to be building nice muscle on his right hamstring, but not his left. We got therapy done on him, turns out he was out of place back there, his sacrum was angled down, his hips were slightly out of line and a fair few other things. Turns out, cause of how out of whack he was, his right hamstring was helping to support both his back legs, and cause of how out he was, he didnt even have any glutes built up, had no glutes at all, so i have to do exercises with him to help build them up correctly. Since the therapy he has been much better, starting to get a bit stiff at times again, but that's cause he'll need therapy done on a regular basis to help fix it. Was told he'll also take 6 months to even his hamstrings out again.
So maybe it could be possible she could be a bit out of place somewhere that is causing some discomfort?
Hope you'll be able to find out soon :)