I've just joined super user, and I've associated my super user account with other accounts (at least one of which has >200 reputation), but my SU account still has a reputation of 1. Is it working like it should?
You have to associate from the side which has more than 200 rep. It's worked fine for me every time but I always initiate the association from SO. I'm not sure if there is a way to disassociate.
From stackoverflow blog:
Be sure to visit the accounts tab of your user page after you join, so you can get the +100 account association bonus on Super User! (Note that this requires at least 200 rep, so be sure to initiate the association from the site where you have at least 200 reputation.)
So you shouldn't make the association from the superuser site.
I have not had any issues ever with associating. Every time I have associated accounts, I gained +100 (100 for SO, SU, Meta, and now SuperUser).
I also get 100 association bonus. In fact, I got it the first time on my stackexchange account in stack overflow. After that, everytime I sign up somwhere I got extra 100.