Domain Mapping: wp-content javascripts and css

I have enabled domain mapping on However, it appears that the domain mapping filters (namely site_url filter) aren't being applied to wp-includes/script-loader.php for when it calls (line 52 & 421 : site_url(); This is causing some assets to be loaded from the wrong domain (the original unmapped domain). This is not a problem in plain text mode, but the assets are blocked entirely (or cause warnings) when loading the site through SSL. I am unsure how to get _all_ assets loading from the correct domain.