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Inhertance of eye color

Dear sir,

I have got a query about how genes are transmitted from parents to kids.

The situation is: I am blue eyed, my mother is green eyed and my dad is brown eyed. This far so good, no problems: I thought,my mum is green(G)-blue(b) and my dad is brown(B)-blue, so I had 1 out of 4 of turning out being blue. It's normal because there are plenty of blue eyed people in my family.
The problem is...just that. From my dad's side, his father was brown and his mum green(her father blue,her two siblings blue). If my father had to pass blue to me and I'm a male, I'm getting his genes from the Y half of his dna 'staircase' (the chromosomes 15 and 19-or even others-carrying the color info are autosomal,different from the Y(number 23),but 'on the Y half' of the dna chain I mean).
Therefore, he's got blue on his 'Y half', but his mum could only pass green or blue to his 'X half', therefore my father should be green or blue, but never brown(he's dark brown,not even hazel or amber).

1)What's wrong with my reasoning?
2)Did some genes from the X side 'swap' with the corresponding ones on the 'Y side' in my father(eye colour, etc.)?(at fertilization when my dad was 'produced'?, at generation of his spermatozoos?
3)If this happens or whatever it is,what's roughly the likeliness for this to happen?(much less than a 1/4th I guess!)
4) Should I infer from all this my father is not my biological father?

Many thanks

Solution Summary

Eye color in human is a polygenic trait. It is controlled by 9 pairs of polygene. If all genes are present in recessive form the eye color is blue and if all are dominant the color is black.