This is similiar to this question except it's not about reputation.
In fact, I agree that different sites should have different reps, it's more the fact the system has to log you into each site manually. I would've thought a more logical approach would be to just have one logon mechanism which logged you into all SE sites.
Not only that, if you want to participate in another SE site, you have to register again - it's only a few clicks, its just weird you have to do it at all, esp now there are about 50 or so sites. Even when you're already logged on and you jump you across to another site, it requires that you refresh.
So this isn't a complaint. None of these things stop me from doing anything, but they are things that require the user to do a tiny bit more. So more just out of curiosity, why doesn't SE have a single sign on system? Is it a design restriction made when SO was only one site that cannot be easily overcome? Is it an intended behaviour? Like some sort of symbolic boundary to let the user know that they have moved to a different area of SE?