First, sympathies on this problem. My boy was lame this spring, and it made me absolutely sick with worry. So I understand that.
I don't know if this will be helpful at all, but when my guy went lame 1) it was a consequence of an old injury, like EnglishElegance suggests. He had an old suspensory problem that hadn't shown any signs of producing current lameness, until 2) I started riding him this spring *without shoes*. At that point, he was not lame at the walk under any circumstances, and he wasn't lame at the trot until we'd been trotting for a few minutes. Even then, it was something that I could totally FEEL but was hard to see. His trot looked absolutely fine when I was lunging him, even with his tack on. But I could 100% feel that there was something off with the trot. I got my trainer to look at us trotting, and even when she was specifically looking for the problem she still couldn't see it until I put him on a 20-meter circle. Then she could see it, but considered it "subtle".
It didn't feel subtle at all, riding him.
So I called the vet, who felt a little bit of puffiness (but no heat and no pulse) around the suspensory on that leg, and after the lameness exam where I was trotting the horse in-hand up and down the drive, he said it was pretty strange - he *still* couldn't see the lameness but he could *hear* it.
I had the farrier out instantly for shoes, put Huey on turn-out "rest" (no restrictions on his activity in the turnout), gave him 10 days worth of bute from the vet, and then started with graded exercise - heat on his bum leg for 10-15 minutes before any activity, then lunging in tack for 10 minutes, then riding at a walk for 5 minutes on day 1, 6 minutes on day 2, and so forth, and no trotting at all for two or three weeks, then working up from there.
I'm happy to say that there's no sign at this point at all of lameness - he's as sound as he's ever been to anyone's knowledge here, and we work for 30-45 minutes 5x per week now, W/T/C.
It was scary when I realized something was wrong, and the rehab was flat-out boring. I was bored, but Huey was even more bored. But we were both patient with it, and even though I had to ride with a wristwatch on to check the time to a minute, we did it, and now it's fine. I learned that I can't ride him without shoes, and that I need to bring him back into work very slowly at the beginning of the season, and I got a pair of Back On Track standing wraps that he wears while I'm grooming and tacking him up.
I hope your problem turns out to be as easy to fix.