Has your kit has been republished since adding the new domain names? If you aren't sure, go to https://typekit.com/account/kits and click the Republish button next to the kit. The fonts will start working on the new domains within a few minutes of republishing.
If that doesn't solve the problem, please share the URL of one of the sites where fonts aren't loading for you. You can email Typekit Support directly at email@example.com if you don't want to post it in the forum.