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A leader defending in an amphibious combat will roll 2 dice TWICE. The reason to roll 2 dice twice instead of 4 dice once (1 cv x 2(because leader) x 2 (because defending amphibious)) is you need to kill the leader if it rolls a double. And if you were rolling 4 dice you wouldn't be able to apply that rule.
You might very well be right here, and if this is how the majority of people play I'm happy to accept that. But as no clarification in the rulebook exists about how leaders roll during amphibious defense, I'm still a little uncertain. Originally I was thinking just as you are, and even surmised that you'd have to roll 2 dice twice to resolve leader combat (though that isn't hinted at anywhere in the rulebook). But when I saw the rule saying you roll at twice the CV (and the CV for the leader is '1') and then the rule that says you roll two dice during combat... well... a little is left up to interpretation with how these two rules gel.
That being said, you could very well be right.
EDIT: Actually, the semi-official FAQ in the Files section states exactly what you said: that the leader rolls two dice twice. The author of the document (C Sandifer) said that designers Tom and Grant Dalgliesh looked it over and approved it, so I'll go with that. Odd though that this FAQ states only units of the same type can trade CV steps and yet Tom Dalgliesh said somewhere else in the forums that units could trade with any other unit and that unit type did not matter. So there's even confusion there!