"Aggregate and compress CSS files" and "Aggregate JavaScript files" in performance settings, is not working
Well, this issue is ongoing at http://drupal.org/node/986558 . The Drupal-7.9 should have fixed it, and it did fix my css, but I am still having issues with js.

Note: if you have this problem and upgrade to Drupal-7.9 , make 100% sure you replace all of your .htacess files.