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Some times, when there are new comments to one of my posts, I get a banner across the top of the page telling me about it. Other times, the envelope beside my name turns yellow. I think I have seen both happen simultaneously once. I am confused about this. Why some times one, other times the other? It seems like the site is trying to tell me something, but I can't figure out what.
I think the little envelope lights up when you have new comments on your posts, and the banner appears when you have new responses (answers) to your questions. The idea is that a new response deserves more attention than a new comment, and the banner is more eye-catching. As Alberto said, the envelope has some lag, and based on discussion at meta.SO, I don't think that will be fixed any time soon.
@Anton: No, that doesn't fit my observations. The comment on this answer produced the banner, but the comment on this one produced a coloured envelope. And in case I remember those wrong, I have asked only one question so far, and none of the answers to that one have been edited in the past two weeks. And I am positively sure that I have seen both the banner and the coloured envelope in the past couple of days.
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