Hmm.. im thinking you may need to start from the begining.. start with trot poles until she goes perfect then continue from there.. maybe she wasnt properly educated and she's not sure how to do it properly anymore? If you need any help message me..
The picture you posted on the Equitation thread you mentioned she was over jumping there? Do you mean over jumping as in jumping a small fence like it's 5 feet, or always taking the fences long? Because in that picture, I don't see her as over jumping at all! :) I see that maybe she took the distance long, but other than that she looks adorable and has alot of talent.
I'm not sure there's a specific exercise to not make them jump big. I suppose the more you jump the more confident they feel and they wont feel like they have to try so hard. I think you should be grateful for a pony like that. One that is careful, round, and uses itself! :)
Now if you are referring to taking long distances all the time, try slowing your gait. Slow it a good amount, and keep that pace right on through from your approach, over the jump, and on landing. Stay quiet in your body and allow her to figure it out. If you are coming up to the jump, and you feel she's going to launch, steady her a bit with your body and reins and see ifyou can encourage her to add in another stride. :)
Does she have eye problems? A horse that is having problems seeing will always over jump because they don't want to hit the fence. Next time your vet comes out, ask them about it and see what they think.
If it's a behavior/training type thing, try grid work. She won't be able to over jump if there is a fence immediately afterwards, she'll have to learn to take it easy in order to make the next fence ok.