My first question, is do you use rear boots on your horse? If not, you may want to start. I used to have a horse that if he didn't have his rear boots on, he would stop on his front end, but if he did have them on, he'd slide in like a reining horse. He did that because he burnt his fetlocks sliding to a stop one time, so he started stopping on his front end. Also, you can try asking her to back up right after you stop her, every time you stop her. Start at a walk and work your way up through the gaits, always asking her to back up several steps after you stop her. This will set her up to stop on her rear end instead of on her front end.
If that doesn't help you, I would work on your seat. Concentrate on keeping your heels down, and sitting deep in the saddle. Also, do you have a back girth on your saddle? If not, the back of the saddle may be popping up and tossing you out. Get a back girth, that will keep the saddle from vaulting you out.
Hope this helps you out.