I've tried to use %invitecode% in each of the two email customizations and I'm finding that it is not being passed for either. I've got the plugin settings set such that an Invitation Code is required. During registration, it is rejecting wrong invitation codes and it does seem to be representing them in the dashboard OK. I haven't tried all of the email replacement keys, but the ones I've tried all seem to work fine except for this one. It doesn't give wrong information, it just seems to be a null.
Also, if I enter a re-direct in the configuration screen and then use the %site-url% replacement key, the re-direct shows up in the printed substitution. I've disabled using it for now since I'm not thrilled with the way that looks in the email. Is this part working as designed?