Some new cancer drug side effect? Or lingering "continuity-fluctuation" as a result of having Card backwriting his childhood? (If it is the latter, don't be shocked if he's a black woman for a panel or two down the road...) Maybe he's really Ultimate Mystique, and this was just a really, really subtle clue.
The same reason Peter Parker's eyes always change color( since his creation during the 60's they've gone brown to green and back!). Or you could use a cool excuse, like he was wearing contacts (Remember those laser omiting ones he had in heros reborn against Whirlwind?).
I think it has more to do with emotions. Do you notice whenever giantman and cap fight eachother tha giantmans eys go red. And when eyes are blue it's more of a calm state. i think this is more hitch than it is millar.