[Plugin: WordPress MU Domain Mapping] Domain Mapping and CSS/JS files

Hello!
I’m using the Domain Mapping plugin for a new network we’re setting up. Some of our sites will be at sub.primarydomain.com while others will be at theircustomdomain.com. All of the subdomain sites are functional and working properly.

When I try to convert a subdomain site to a custom domain, however, the site loses references to both theme and backend stylesheets and JS files. All of the content is loading though. Any ideas what the issue might be?

Thanks in advance,

Daniel