The way StackExchange.com leagues work are fairly simple: look at the total now, use that value, do the same tomorrow, the day after, etc.
Leagues are calculated from one day to the next by looking at the total reputation each user had. Now, unfortunately that means when a user's rep is recalced on the site-side of things (where we do fix all history), the net total difference from this interval to last on the league side won't match up if there was a change.
In this particular user's case he was affected a great deal by a bug in the system from quite a while ago where votes didn't always line up to the posts owners. This was fixed, and resulted in a recalc for all affected users (around 2,000 on SO). As you can see from this user, some of the oldest users got a measurable rep boost from these previously-unassociated votes.
At the time that recalc happened, Cody went from 10,648 to 13,594 rep...which is the jump you see in the "total-only" league view.
I'll talk with David today and see if we can do anything about the leagues, it's not a simple operation to fix history though so no promises there yet.
Update: David recalced the user's reputation leagues on the SE.com side, all is well now.