Actually, this is super-weird.

This feeling of 3D "coming out" of the screen is caused by a thing called "negative parallax", and things receding into the screen caused by "positive parallax".

Avatar actually had a comparatively mild amount of negative parallax, compared against things like Jim Carrey's A Christmas Carol, which was LOADED with it.

Negative parallax can look really bad and cheap very easily. It takes a light touch to make it look good. Avatar did it really well and used it sparingly, so that when it DID happen, it surprised you - the "duck and cover" moment. Other, shitty movies use it everywhere, to the point where you no longer notice it - the maximum negative parallax becomes your 0-base (subjectively).

Just a little anecdotal evidence here, but I also saw Alice, Avatar and Clash of the Titans, and both Alice and Clash gave me headaches, but Avatar did not. Actually I thoroughly enjoyed Avatar's 3D experience.

Just my .02 cents

I think different 3D technologies could account for the in-ness and out-ness. Where you at the same cinema both times?

Actually, it was - same specific cinema. But weeks / months apart which could impact things - good thinking.