However, a month or two later when Google's webmaster tools and Moz acknowledged the redirect for the old's site the links were not attributed to the right domain.
For some reason they were attributed to my "default" domain that has been setup on my nginx server.
I've tested clicking a lot of the links from the old domain and they all properly redirect to the correct domain, it's only the webmaster tools do not.
Any ideas? I tested a lot of links and they all redirect properly. Now I'm stuck with inaccurate keywords to the wrong domain and none to the correct domain.