For those of you who don't know, "hajimemashite" is a ritual phrase that loosely translates to, "it's nice to meet you." You usually only say it the first time you're meeting someone, because it probably comes from the verb "hajimeru," which means "to begin (transitive)." The "mashite" makes it polite, and gives it the more literally meaning of, "beginning [our relationship]..." Or something. This is all stuff I came up with last night, so I don't know if it's accurate. Seems right though.
"ja nai" is a negation, to say, "it's not hajimemashite," the "desu" makes it polite, the "yo" makes it emphatic, and the "ne" indicates that Dark knows just as well as Satoshi that that is the case. This is probably why I seem to remember it being translated as, "This isn't the first time we've met," or, "This isn't the time to say 'nice to meet you'," or things like that.
There's really not a whole lot wrong with these translations, and I remember seeing the episode and thinking how much of a pain it would be to have to be the one translating that. I also remember thinking that we would have to translate it similarly and just be sad that all the non-Japanese-speaking viewers would have missed out on a really cool line.
But, since we had had aspirations of being people in charge of translating the DN Angel anime, as well as the manga, we thought about it. And then Athena came up with the most brilliant translation of it, and we're a little sad that the translators at ADV didn't come up with it, but a little too proud of ourselves that we did.
"It's nice to meet you... again."
Or even, "Pleased to make your acquaintance... again," but that's a little wordy. So anyway, it's true what someone said on the Honyaku mailing list: a translation is never complete--it's only the deadlines that make you stop. Sometimes, a direct translation is not always the best one.