Same problem here, 1 eye is simply like 15ms out of sync (and focus) with the other, for me 3D works great, it just causes me intense headache after a while and a feeling of dizziness .. well it was Avatar and that movie is fairly long and has great 3D... but that was the first and last one for me.
The funny thing is, the 3D technology isn't really "dead"
If someone invested proper money in a dual-display that has left/right screen and ability to measure and sync to our eyes separately it can work for a great many people. Your eye issue Volatar is even among the rarer eye issues rare.. for most people the 3D headache is a simple "timing/syncro" problem, simple as in.. its easy to find.. but its extremely difficult to properly sync a device to a single eye and another device to another eye.
By the way, the other issue with 3D is the way its layered, for this to be really fixed and watchable the movie would have to be literally rendered as shown and not post-edited so that the 3D is in layers (which currently is required because of the brain-dead technology) (Just so you understand this, this means a movie would essentially need to be rendered twice, once for each eye
I got no reply yet by way