When you put the saddle on - do you make certain the front of the saddle by his withers is not on top of the shoulder blade? That's a common mistake. To check, before you tighten the girth, see if you can run you fingers round the top of the shoulder blade. If not move the saddle back - you should have about 2 fingers worth of gap between shoulder blades and saddle.
If he's starting to do what wasn't done before it usually pain (saddle no longer fits because horses muscling has changed, or saddle is not placed on horses back properly, etc.), rider is doing something to inadvertantly tell horse to stop, or a training issue. It is rarely a training issue, so if you can run your fingers down horses (bare) back and he doesn't flinch away (as in "Ouch") then saddle probably fits OK, look at legs. If vet can't find any pain then tell your trainer you believe you are doing something wrong - so ask them to ride the horse. Do they encounter the same issue? If they do (more than once) then could be a training issue. If they can't ride the horse find a very good rider who can.