Yeah, it's strange and confusing. Basic profile information like e-mail address, OpenIDs, etc. transferred over, but "Member since x date" and reputation, etc. all got reset per site.
And that kind of sucks, since some of the basic privileges like commenting or posting links, etc. have to be earned through reputation. If I was a well-known, reputable user (e.g. over 9000! rep) on Stack Overflow and suddenly wanted to chime in with a helpful answer in (e.g.) Mathematics, then my ability to do so as a new member to the Mathematics subsection would be very limited.
It's kind of like living with your parents, needing to earn their trust to do anything, except the amount of trust they have for you varies depending on which room you happen to be in when you ask them.