Some of my questions and answers have been voted on (both up and down) on this meta site. Why doesn't my reputation change, like it does on the primary Meta site?
Reputation is always inherited from the parent site. You cannot gain or lose reputation* on the per-site meta. This also means that some reputation related functions like the reputation graph, and bounties are not enabled on the per-site meta.
Voting up or down does not affect reputation. You are now free to vote purely based on post content, without worrying about how your vote might positively or negatively affect someone's reputation score.