You could have a subtle problem with using your eyes together that went undetected. That was my issue, my eyes weren't pointing in quite the same direction so they gave me prism lenses to correct it and I can now see in 3d. Still have trouble differentiating objects from each other, but that's a brain thing in me not an eye thing.
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"In my world it's a place of patterns and feel. In my world it's a haven for what is real. It's my world, nobody can steal it, but people like me, we live in the shadows." -Donna Williams