It sounds like something is wrong with URL rewriting and not actually your Theme stylesheets. Click the Create secure.htaccess File AutoMagic button and activate root and wp-admin folder BulletProof Modes. If that does not fix the problem then check your BPS Security Log and post the log entry that shows what is being blocked.
Also did you reactivate all of your Plugins on the WordPress Plugins page? Maybe one of your plugins does something with the visual appearance of your site? Or your Theme uses a bundled Theme plugin that does that?