I too considered this as a possibility, but after thinking about it, I don't think it should be an excuse.
If you don't count the goalkeeper and the two CBs, for which it doesn't matter what formation we play, you have 8 players left, of which 4 are newcomers (Grosso, Caceres, Melo and Diego).
The other 4 are the 2 attackers (when we play 4-3-1-2), Camoranesi and Sissoko.
Amauri played big part of his career as a lone striker, so I don't know why should he, after 1 single 4-4-2 season, not adapt to a different formation.
Sissoko played in many different formations too before he joined Juve.
That leaves Camoranesi and the other attacker as the only ones who are used to playing 4-4-2.