I use the Odyssey Two-Ball as well and I don't have a problem like yours, so I don't think it's the putter, but it can very well be the angle of contact with the ball.

If the ball is forward in your stance, you might be hitting it on the upswing, and since most (if not all) putters DO have a little 'loft' (something like 3 or 4 degrees), that might cause the ball to lift when you hit it firmly for longer distances.

Try to put the ball in the very middle of your stance or perhaps just ½" back, so that the putter will be on the downswing as it strikes the ball.

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//Mox
2008 bag:
Mizuno MX-500 460cc 10.5* Fujikura Tour Platform 26.3 stiff. (about to be replaced by MP-600 10,5* UST Proforce V2 stiff)
Mizuno F-50 3w 15* Fujikura Tour Platform 26.3 stiff.
Wilson Deep Red 5w 18* Graphalloy Fatshaft stiff
Cleveland HALO 3i hybrid 22* graphite regular
Mizuno MP-60e forged 5i-PW True Temper Dynamic gold R300 steel
Mizuno MP Black OX raw haze 50/6 GW, 54/9 SW, 58/10 LW
Heavy Putter B3-M
Titleist NXT Extreme