Basically everything works fine except for the top level pages ( e.g. category,archives, single post, custom post type, etc…).
I have 3 custom post types and a 4 custom taxonomies (each custom taxonomy is attached to a post type respectively and there is one more taxonomy that is attached to all of the post types). In addition, the custom taxonomies have a rewrite set to ‘/’ to just show the term and not the taxonomy itself.
Any thoughts as to why this is happening?
UPDATE:
So after having just post this after a while of looking for why this was happening, i found out the problem. In the reading settings, my front page was set to be displayed as a static page, and when i changed it back to the default, everything worked fine.
This can also be solved by changing permalink settings, you can change permalink settings to Plain and save settings, then check your pages. It will show up by now, once done, revert back your permalink settings to Post name and save settings. In this way your pages will be shown properly.