I was just looking at my list of accounts and was puzzled to see that Stack Apps appears twice. No other site appears twice. When I hover, the user number in the link is the same for both lines. This happens whether I click Accounts while on my Meta profile or my SO profile. In fact, it even happens on my Stack Apps profile.
At the bottom of the accounts tab on your profile, there's a button to clear the associations. Do that, and then re-associate your accounts. That should clean things up.