If I were you I would get a second opinion on the saddle, get a chiropractor out (McTimoney-Corley are awesome!) and perhaps do some carrot stretches in the meantime to help stretch off any knots?
Most horses that look like they have shoulder problems have foot problems and tbh 99% of lameness comes from the foot. This has been covered on posts previously which is why I know this little fact. My suggestion would be to have a lameness workup to assess exactly where the horse is lame, using nerve blocks to find painful areas. This can be arranged by any reputable vet and insurance companies would normally cover this. This would personally be my first port of call. It does also sound like he could have a possible back problem and maybe a chiropractor would be a good idea, Mc Timoney Chiropractors are very useful for example. If the horse had Kissing Spine I would expect to see reluctance to go forwards when ridden, bucking, resentment at girth being tightened (you say he doesn't like his saddle put on, is it because girthing is an issue?), refusal to stand still when mounting, continually cantering disunited, or swapping legs on one rein, and just an unhappy horse in general. Usually (although not always) Kissing Spine can come about by a horse not working through from behind correctly due to hind limb lameness which is usually (not always) attributed to hind suspensory ligament issues. I went through all this with my horse who I was convinced had kissing spine, but it turned out to be rotated pelvis, and sore muscles (the ones that run from the back down to the girth area - sorry forgot name) and mild bone spavin on both hocks which he has been sucessfully treated for, although obviously this will always be ongoing. I've also gone from a synthetic saddle to a correctly fitting and comfortable (for horse) second hand leather saddle which has been worth its weight in gold, although it nearly cost that much at the time! Kissing Spine seems to be having a lot of press at the moment and I know of loads of horses that have been diagnosed with it, but I expect that is because there is now the technology to come up with this diagnosis whereas maybe ten or fifteen years ago this was not possible, or only an option of a selected few people who could afford to have it done privately. Most people, like me, automatically think a problem is KS when in fact sometimes it is nothing to do with that at all.
Speak to the owner of the horse and find out if she's had the vet out. You say the saddle has been checked and it fits fine, but was this with a rider on board, and was this check done by a qualified saddle fitter? It is hard when a saddle is borderline to know if it fits correctly or not if you are just a layperson.
I will find out whether the saddle was checked with a rider on board or not.
Yes he doesn't like his girth being done up, I always do it up very slowly and gently but he is always very tense and has been known to rear in the past. He is also very tense and reluctant when he is mounted.
I guess it could be anything, I just thought KS because he feels very stiff through his back as he walks. (You can almost feel something locking and unlocking in his back. ) He is currently being treated by a McTimoney Chiropractor so hopefully this should help. Another Chiropractor in the past has also said that the reflexes in his back are the wrong way round. The horse is a riding school horse so has obviously ridden by lots of different riders so he really could have anything wrong.
armchair_anarchist - The pony is not being worked. He was being worked when he wasn't lame, he was just very tense so there was obviously a problem. When he went lame he was rested and as this didn't help he was seen by the Chiropractor a few days ago, and were told to work him lightly a couple of days later, mostly walk and a few gentle trots) To see how he is.