Two different Animus's.
I believe it is stated he simply wrote a hidden code, that appeared as glyphs, in the base of the Animus's Programming so when the Assassins copied the Animus they also copied the hacks.
I just wonder what kind of relative 16 is to Desmond and how much of his memories are encoded into the Animus
I wonder what will befall the characters in this game? mmmmm
"What part of I AM BUSY don't you understand? Is it the "I" bit? That refers to me. Is it the "am" bit? That's like a "doing" thing. Is it - is it "I'm busy"? I'm busy!" -Shaun to Desmond (jeez Shaun O_o)