Update: The new system for dealing with association bonuses is now deployed across the network. It's more reliable, faster, and simpler. I also ran a backfill of association bonuses that should have taken care of anyone who should have one anywhere on the network (please comment here if you find an exception - I'll take a look).
Now for the bad news: I'll be running a much sadder job tomorrow to clear up a few thousand duplicate awards from the old system, which suffered from some race conditions, so a few illegitimate +200 bonuses will become +100.
This is the result of the association bonus being completely on the fritz. Honestly I couldn't figure out what's going wrong with it after 2 hours of investigation, so I stopped.
Even if we fixed the current method of doing this, it would, by nature of how it works, still break - during builds, etc. Instead of spending another several hours trying to track down what the hell's happening, we made the call yesterday to replace the mechanism that does this completely.
We did a lot of network account work several months back which means how association bonuses work can be much simpler all around (from a high level: we don't need to track network level things on each user). We can now enjoy the benefits of that earlier effort in other network-level things like association bonuses.
Apologies this is taking more than a day to fix, it's just not a simple thing to do. In addition to the core Q&A engine, it requires changes in: StackExchange.com, Area 51, Careers, StackAuth, and API v1.
We've completed most of this, but need to test and I need to write some backfills to fix people both affected in the last few days, and affected from wayyyyyy before that (as I said, it's always been buggy). I hope to roll this out this afternoon/evening after we give it a good thrashing in the dev environment.