Shooting with an AndyMark pneumatic wheel gives you the benefit of a nice compression coupled with tread that is VERY grippy. It doesn't sound like your 6" tires are gripping the frisbee enough. In some of our earlier shooter prototypes, we experimented with plaction wheels from AndyMark, using various types of rubber/foam materials purchased from McMaster-Carr as our tread. If you'd like to experiment as well, Part # 5109K55 is a good place to start. Just rivet the foam strip (after cleaning it with alcohol) to a plaction wheel as you normally would with wedge/roughtop tread. I'd recommend putting a small washer on the rivet before you place it in the wheel, as just rivets alone will tear right though the soft material.
I don't know how well this stuff will wear over time, so your mileage may vary.
Try experimenting with compression of the frisbee, as well as shooter wheel speed.
Here's a team that's seen lots of success using very small wheels to shoot:
http://www.chiefdelphi.com/forums/sh...hreadid=111360