At least for me it says I have the same reputation on both the main Apple.SE site and meta.
It's by design: Upvotes and downvotes have no effect on your reputation in the per site metas (everything but MSO).
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 rep graph and bounties are not enabled on the per-site meta.
See http://blog.stackoverflow.com/2010/07/new-per-site-metas/ for more information, also check out a related question on MSU: https://meta.superuser.com/questions/1255/how-does-the-reputation-on-parent-and-on-meta-site-work