I recently opened an account over at https://softwareengineering.stackexchange.com/. I associated my account there with my account here. I then opened CStheory again, and I got a red banner saying "You've associated your Theoretical Computer Science and Theoretical Computer Science accounts: +100 reputation". I made a printscreen in case it turns out to be useful.
This is obviously a bug. I'm almost sure this 100 rep was intended to be awarded to the account I just created. My account on this site gained 100 rep (I went from 358 to 458).
Edit: I tried reassociating all my accounts as per Tsuyoshi Ito's answer, which gave the missing 100 rep to my Programming account. I still have 100 too much rep on my CStheory account though.