OMG - I have a similiar situation. My 4 year old pony has been lame for 5 months. Front left shoulder. He had 4 weeks of bute and stall rest. He was then sound on the lunge line and put out to pasture for another 2 weeks. Looked fine. But not quite right under saddle. So, we walked him a lot under saddle. No improvement. A few weeks later he was practially crippled under saddle, but still ok on a lunge line. Brought him to large university and got $2.5K worth of xrays, sonograms, hole body nuclear scans, etc. and they FOUND NOTHING....ZILCH, except that he was practically crippled! He was lame both in the right hind and the left front now! Go figure. Vets are all scratching their heads.
I hope Faye is right - he is now turned out with 3 other other older gentleman in a lovely pasture. He runs around like a lunatic, through the snow, sound as can be.
He has been lame for 5 months now. This is so frustrating.