I have witnessed this in early beginning watching 3D and found that the images were switched--ie. L/R was R/L. I had to select that the images be switched back. That said, sometimes it's in the glasses themselves. Some will work fine, while others are always out of sync. Could this be your problem?
The other thing to try is to measure the distance between your pupils. It should be about 2.5". It's the separation for infinity that is used by cinematographers. If your separation is much greater or less, then you might not see 3D the same way that the average person does. Either way, it should not be something to worry about. Just enjoy what you can and be thankful you have two eyes and not one .
Another influence is the size of your screen and how far you sit from it. A smaller screen will have less separation and change the window. Or try increasing or decreasing the separation in your bluray player if that is a feature--my Sony player does this. Also, sitting closer will compress the 3D decreasing depth between objects and sitting further away will elongate it--adds more depth between objects. Try moving your watch zone.
Edited by TVSTAR - 1/6/14 at 10:36am