Yes that happens to me too! You have to restart your xbox a few times and then it will appear again. I don't know why but it's like every third time a restart my xbox the 3D mode becomes available.
It's not the greatest but if you play on the zoomed camera view it gives you the most 3D effect. I cant wait until games start utilizing the NEW 3D tech because that will be very cool IMO. This is the old style of 3D with the colored glasses. Red & Cyan works the best. I tried red and green and not so good.