Stifle problems are due to a lack of strength in the stifle, not saying that the horse is out of shape just that that particular area is under developed. If it is a stifle problem then the coarse of exercise that the vet I worked with recommends is lots of trotting and walking collected in deep sand (avoid cantering/loping as it does not help), collected backing, backing up hills and if the horse will allow having them pull a tire or log. You will want to do these exercises for 20 minutes 3-4 days a week minimum, for a month. Along with the exercise you could also try estrogen injections. This will tighten the tendons and ligaments up. There are other things that people do they have been known to blister the stifles but she is a young horse and I don't recommend that.

She is also at the age if you use her alot that she could start fusing her hocks. Does she give the farrier any problems when he does her hind legs. IF this is the case the cheapest way to fuse the hocks is bute her and ride her. A faster way is to have them injected with a steroid.

The only other thing I can suggest (and we tell our clients this) is get the horse sore and then see if you can take her into the vet that day. So they can see what you see. OR have someone video tape you riding her when she is doing it. Some horses don't show things when you are doing a lameness exam in hand. But as soon as you get on their back they show the problem.

Hope this helps.