Very interesting and puzzling situation. This is all armchair speculation, but if I were to try to figure out what might be responsible for phenomena as you've described them, one area I'd be inclined to learn more about and address with an appropriate medical professional would be common opponent processes in the visual system. This would be accomplished by the neural circuitry throughout the visual system - all the way from the retina and extending throughout the visual cortex. For example, a blue vs yellow center-surround antagonism is a generally accepted feature of the magnocellular pathway the visual system. A similar red-green antagonism is well described in the parvocellular pathway and you may find more abundant resources detailing how that works.
There would of course be many other features of this condition to look into as well, including the signal amplification and dampening that occurs to aid in the discrimination of boundaries / contours in the visual landscape, etc.
Understanding the neural circuitry of the visual system happens to be an area where a lot of academic progress is being made, which means there is a lot of information out there. That can be both good and bad when you try to sift through it all, though. I just put a few things in bold/italics that might make for good search terms if you want to seek out more comprehensive resources.
Wanted to add: If finding good resources explaining the anatomy & physiology I mentioned proves to be tricky, let me know and I'll try to find something good in the public domain next time I drop by here