To help me better understand what the issue is, can you show me a screenshot of your widgets and their Visibility settings, and possibly link me to your site, as well? You can use http://snag.gy for the screenshots, and if you want your site to remain private, you can send us the URL via our countact form: http://jetpack.me/contact-support/
Just remember to oinclude a link to this thread if you contact us via the form. Thanks!