If your horse wouldn't stand for flexion tests, then your vet is right it's likely pain related in the hock or stifle (unfortunately you have to be able to do the full set of flexion tests to help narrow down where the pain is). If your mare wouldn't stand for flexing, then your vet really couldn't do anymore with a physical exam and had a general region that needed to be examined more in-depth. The only way to do this is going to be x-rays of the hock and stifle.
As for what should be done now, you don't know what is wrong and without knowing you can't know what needs to be done. For some conditions turnout is going to be best while for others stall rest would be best.
If you want an answer, rather than spending money on this or that kind of alternative practitioner (who may have very little or a pretty good education), you need to go ahead with the lameness exam and get x-rays of the leg.
Right now she is on stall rest with hand walking every other day. When it stops raining I am going to turn her out so she can move around. Tomorrow (sat.) I am going to take her out in the arena and see if she is still off and how she is looking ...
Twende I thought about the chiropractor ... I might try that, thanks for that advice!
Ill keep you guys posted...