I just created an account at outdoors.SE (via MyOpenID) to answer a question migrated there, and noticed that I had 1 rep, despite having over 200 rep on several other StackExchange network sites, which should let me start from 101 rep.
My user profile does list several linked accounts (including my SO account with 5k+ rep), so that's apparently not the problem. However, I did notice that the e-mail and website fields in my profile were not automatically filled, so I had to add my e-mail manually to get my usual gravatar.
Just to confirm that it wasn't an isolated problem, I went and created an account at cstheory.SE, where I also didn't have one before (this time via StackExchange OpenID, since MyOpenID wasn't working), and experienced the same issue. So it appears that this bug is reproducible.
Addendum: While writing this post, I went back and reloaded my profile page on outdoors.SE, and it appears that I now have 101 rep there (and a message bar congratulating me for gaining "create chat rooms and 9 other privileges"). However, cstheory.SE still shows me at 1 rep.
Edit: I just noticed that the new reputation page now shows the "Association Bonus", so I checked it out. Apparently, I created my outdoors.se account at
2012-03-12 21:07:59Z, but only gained the association bonus one hour and 47 minutes later, at
2012-03-12 22:54:33Z. On cstheory.SE, my reputation events list is still empty.
Why isn't the association bonus applied immediately upon account creation? I'm pretty sure it used to work that way, and the current behavior seems like a significant user interface regression. If I create an account on a new site, it's because I want to do something on that site that I can't do just as well without logging in — not because I want to wait two hours and then come back to do whatever it was I meant to do.
Edit 2: It's now been over 12 hours since I created an account on cstheory.SE, and I still have only 1 rep there. Apparently, something more than just waiting is now needed to trigger the bonus.
Edit 3: My 100 rep bonus on cstheory.SE was finally awarded just one minute before Nick Craver posted his answer below. However, my stats.SE account, created 20 minutes ago, is still at 1 rep.