If you have tried to disable notifications via NewsSquares' notification window - it won't work properly (sorry Chrome bug! haha). Please go to our options page to disable notifications instead. If in some cases NewsSquares get disabled instead, please go to "chrome://extensions" then find "NewsSquares" and click "Enable". It should be back on the new tab page. It's kind of funny, we know, but please forgive Google - Chrome's App functionality is new!
You can actually manage your subscriptions in a one screen interface. Just click on the manage button in the Add dialog. :P
Thanks again. Enjoy!