But if you're using side-by-side, the TV should be telling you that it's 1080p, not 720p. Once you enable side-by-side 3D from the Tridef menu, you should see the screen divided into two instances of your game, one on the left and one on the right. Then, you enable side-by-side mode from your TV's menu. Check the output resolution after that.
Also, glad to see you're enjoying the 3D experience. Under the right circumstances, it truly is remarkable.
If you haven't seen the movie Gravity yet, all I can tell you is that you're in for a real treat once it's out on blu-ray.
Btw, did you buy Tridef? Or are you using an earlier cracked version?