When I go to http://careers.stackoverflow.com/cv/edit/, go to the "Stack Exchange" section, and click on "edit" under "Accounts", I see the following at the bottom of the account list (partially truncated for reasons of space):
Now, as you can see from my reputation here on MSO, I should have the association bonus on all sites where I have an account. Yet, for some reason, my accounts on Android, Italian, Sound Design, and Windows Phone are listed as having just 1 reputation. However, if you look at my account on each of these sites (Android, Italian, Sound Design, and Windows Phone), you will see that I do, indeed, have 101 reputation from the association bonus.
At first, I thought the commonality among those four sites was that I hadn't performed any actions on them (not even voting), but it turns out that I have actually cast a vote on Android, so I don't really know what's up.
Note also that all of these accounts are at least a few weeks old (and my association bonus is even older than that), so this doesn't seem like it would be a caching issue or anything.