It sounds simialr to what I and my son have experienced related to amblyopia. I find when things swim, closing one eye helps. I think it is also a case where giftedness aggrevates the issue, as I notice my DS6 would make a confident guess when a little more time might have illustrated that something wasn't making sense. It also kept us in the dark as to his vision problem until the school physical a year ago.
As I understand it, the brain is trained to not trust the integration of the eyes or one of the eyes at an early age due to strabismus, amblyopia, or a huge mismatch in acuity.
Retraining his brain with two hours a day patching made a huge difference for DS. I would hope you find a similar outcome as behavioral optometry seems to have come a long way in recent years.
