Thus, I can't ask this question in meta, since it takes at least 5 reputation. Can a mod transfer this?
I had the same problem. I fixed it by unlinking and then linking my profile a second time.
I have the same problem, so I can't put this as a comment on this question. Regardless of if I need the reputation, it's a bug, so I just wanted to mention I experienced it too.
EDIT - I've got 6 rep now, so I cross-posted a question in meta that links here.
EDIT - xbones: I've got accounts at SO,SU,SF,Ubuntu,Gaming,DIY and others. For each of them, I've always gotten the +100 at the new site I'm using, not the site I'm linking to. If this has changed, then it's changed, but I hadn't heard anything about that.
When I made an account here, I got 100 rep at Stack Overflow, not here. You get the 'linking' rep at the other stack exchange website you're a part of.
EDIT: I just happened to visit Physics.stackexchange again and this time, I got a notification that I got +100 for linking.