We were in the exact same situation as you a few days ago. We added an angled piece of aluminum at the bottom of the hopper. This causes the bottom frisbee to slide partially into the shooter which keeps the frisbee on top from causing a jam.
Here's a few pictures of our practice-bot's hopper :
http://imgur.com/a/f3X46#0
We found this solution to be extremely simple and effective. Before the angle piece our hopper jammed 90% of the time, since the fix it hasn't jammed yet.
