All of the rares in Archenemy are not associated to the set. Every other card in the decks is mapping correctly it's just the rares that are missing.

Interestingly enough, this is because Gatherer also does not list Archenemy rares. Weird...

I have submitted a bug report to them too.

Awesome... That is very odd indeed.

Any update on this?

Yep, as of today, they're fixed: http://deckbox.org/games/mtg/cards?f=5386!634&c=icte