ergophobe - 12:44 am on Mar 7, 2013 (gmt 0)
Generally speaking, you don't want to touch the Drupal base theme anyway.
The Drupal theming cascade is going to always recurse up from subtheme to base theme to system theming. If you declare something in the subtheme and the theme system gets a "hit" there, it shouldn't load the parent theme at all.
If you turn off CSS aggregation in Drupal, you should see all stylesheets that are getting loaded. Can you check to verify that the base theme stylesheets are getting loaded at all?