Did Thunderbolt Ross dye his hair after The Incredible Hulk and why?

In The Incredible Hulk, Ross is a military general; in Civil War, he's Secretary of State.

That means he's a very high-profile figure in American and international politics, and so his appearance matters. A partial dye-job (assuming that's what changed his hair colour) looks reasonably natural, and makes him look less like a doddering grandpa than he otherwise would.

So: probably just a makeover, nothing to worry about. Save that for when his hair starts turning red.