My site also got affected by the latest version 3.x of the plugin.
1) All our users that only was assigned a custom created role, were unable to see any content of the front page etc.
2) Some pages are highly secured so that only a specific role can read the content. For these pages, everyone got 404/not found, even myself when trying access them as Administrator. I was able to see the title of the pages under WP-Admin / Pages / All pages, however, there was not even a link to click in order to edit the page.
When downgrading to the previous 2.x version, everything works again as expected.