Domain Mapping URL Rewrites Are Incorrect

Hi,

I recently installed and activated your plugin. I have domain mapping working almost perfectly. But I am having an issue with the URL Rewrites that this plugin creates.

In my original setup my enqueued scripts use
/app/themes/mythemenanme

Files are also physically available in this location.

When trying to visit the mapped website, the link turns into
//mydomain.com/themes/mythemename

which breaks my site because the word '/app/' is no longer part of the url.

Please advise