only default theme stylesheet is fetched

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Only when mobile_plugin is enabled.

For me, this was a problem with the Mobile Plugin (http://drupal.org/project/mobileplugin) module when using multi-site configurations. I was able to work around this problem by making a minor change to the plugin. Resolution will probably have to be taken up with the Mobile Plugin maintainers. I haven't submitted a detailed bug report to them yet, but I wanted to leave a summary here since I just fixed it on my test site.

The offending code is in sites/all/modules/mobileplugin/mobileplugin.module.

function _mobileplugin_filter_css(&$css = array()) {
        $group_setup = mobileplugin_get_group_setup();
        $filtercss = _mobileplugin_get_setup_val($group_setup, 'filtercss', array('sites/all/themes/', 'themes/', 'sites/default/files/'));

If you're using a multi-site setup, you'll have to add the site's files directory to the array.
Original

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

Modified (subdomain added)

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

Mobile Plugin will need an addition here that makes it multi-site-aware. For now, if you're just running one or two sites, it's easy enough to add an extra value to the css search path.