This statement confirms that the footballs were in fact messed with purposely. So all they have to find out now is who is guilty.
Here's my "theory:"
Indy informed the league about their concerns with the footballs after the November game. The league never followed up with checking the Pats* balls (hehehe...) at halftime or after the game in any of their following games. The AFC championship comes along and pits the Colts against the Pats*, and the Colts make sure that the officials check. Oops, looks like there is a problem.
Of course, I am assuming they have been doing this the whole time, which may not seem fair to some, but I couldn't care less.