Problems w/ themes and multi-site installation
I have also experienced this issue as well. It seems that drupal doesn't want to recognise themes and modules on a multisite subdomain basis (i.e. sites/yoursite.com/themes is ignored!!!). I don't know if this is intended behaviour but the only solution I have found thus far is to put all modules and themes into the sites/all folder and then to check they are enabled in the admin interface.
Drupal will correctly respond to the subdomain request (and rewrite paths where appropriate) so long as you have the sites/yoursite.com folder.