The times Gambit's eyes weren't red and black were due to the colorist messing up, this much is obvious. However, I disagree with the argument that they are not part of his mutation.
Yeah, there were times when Gambit was depowered and his eyes were still the same but also there was that time when the High Evolutionary erased the x-gene. Gambit had normal eyes after the fact. Nightcrawler and Beast were normal looking as well. So his eyes were part of his mutation, at least in this case.
If his eyes are not related to his mutation it would mean that Gambit is not just a mutant but also something else. Personally, I don't like this idea.
If eyes weren't part of his mutation then Rogue wouldn't absorb his eye color with touch or kiss.
And there's also this. Although I don't think there's much thought put into this except for the fact that it looks cool.