When you first mentioned this problem, I thought you might have the same problem that a friend of mine has. Her situation is that she can't do things like look through binoculars, because her brain doesn't allow her to fuse the two separate images she's seeing into one image. Since the 3D movies are essentially two images, I thought it might be the same thing. But it sounds like yours is more literally eye-related, where hers is actually something in how her brain interprets what she's seeing.
Are you still able to enjoy the ride?