According to Stephen Fry, in the TV programme Q.I.
"Aye, Sir." indicates agreement, as in
"Nice day, Number One."
"Aye, Aye, Sir." indicates "order understood and will be implemented" as in
"Pipe 'Hands to bathe' Number One!"
"Aye Aye, Sir!"
Whereas, today's BBC homepage reveals the Q.I. Fact of the day:
"In Amharic, the national language of Ethiopia, 'aye' means 'no'."
Moral: be careful where you recruit your crew.