TV-shows sometimes have mid-season breaks (I don't know why, but that seems to be what they do). White Collar seasons 2 and 3 did just that, as you can see on the [Wikipedia Episode list][1].

I would say that is the most likely cause, and should mean the Intro changed from Episodes 9 to 10 in Season 2, and 10 to 11 in Season 3.


  [1]: http://en.wikipedia.org/wiki/List_of_White_Collar_episodes