A user on the Unix SE ran into a problem associating accounts -- he wasn't getting +100 for associating with his other accounts (even though he definitely should):
I tested it by making a new account on Physics SE, and associating it with my other accounts, but it stayed at 1 too:
Something appears to be wrong with the +100 rep bonus for associating with another account
Edit: For maximum confusion, I found that creating an account on another SE I hadn't been on caused me to get the association bonus on the first site. I signed up for Physics, got nothing, signed up for OnStartups, got the association bonus on Physics but nothing on OnStartups, and then signed up for GIS and got the association bonus for OnStartups (GIS is still at 1). I'm seeing "user associated account: Unix <-> SO" entries in my Unix account history, which I think is wrong since these associations had nothing to do with either of those, but I don't know enough about that