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The color blue
All that occurs to me is that it's not physical, but in the brain, i.e. blue is a pessimum for you. Dr. Bates talks about this with green as an example if I remember correctly. Maybe something traumatic happened to you connected to this color you don't remember. Identification of the problem is the first step to solving it -- nice going! (Or maybe it's as simple as the 2 LEDs are different in more than just their colors.)
Human eyes are naturally less sensitive to blue and purple light than to certain other wavelengths. I think they're most sensitive to yellow-green light. Could have something to do with it.
It's called chromatic aberration. Shorter wavelengths of light are bent more in a lens. You can test this by making an image with three dots side by side: red, green and blue. (I'd post an image but the forum doesn't allow them for me yet.) If you're myopic, the blue dot's blur should be the biggest, followed by the green, then the red. If you're hyperopic, it's the other way around.

There are fancy lenses used in fancy photography that can focus 4 wavelengths of light perfectly at the same time. (google Superachromat) As far as I know, the human eye can only focus one.

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