This issue was originally posted to the mobile_garland theme project. http://drupal.org/node/896072

Mobile Plugin CSS is generated from files found in the following directories.
'sites/all/themes/', 'themes/', 'sites/default/files/'

Sites with multi-site configurations that have customized their color preferences for the mobile garland theme have their css put in 'sites/sitename/files/'. Some means of detecting additional sites and add them to the CSS search list is needed for full functionality in these cases. As a workaround, site maintainers can update the search path with the sites they need.

If you encounter this problem, you can add your additional site to the search path as shown below. This snippet is from around line 30 in sites/all/modules/mobileplugin/mobileplugin.module

   $filtercss = _mobileplugin_get_setup_val($group_setup, 'filtercss', array('sites/all/themes/', 'themes/', 'sites/default/files/', 'sites/subdomain.example.com/files/'));