I've associated my SO and Meta accounts - network profile
However got the association bonus only on Meta, but not on SO. Why is that?
Check http://stackoverflow.com/reputation; on the bottom of the page you should see the following line:
It is right before the line showing the total reputation, and after the lines showing the reputation gained this week, this month, this quarter, and this year.
As I noticed, the reputation page on Stack Overflow doesn't show you when you gain the association bonus on Stack Overflow; only http://stackoverflow.com/reputation can say if you have it, but that page doesn't show you when you have gained it.