The steps are almost already clear. But once again..
I have installed wordpress and used ag admin menu to hide/show some menu items for non-admin user. All was fine. Then installed 'types' plugin and created a custom post type 'courses' with its menus. This disturbed the alignment of all menus for non-admin (as per ag-custom-admin), so I did reset the custom menu. All menus now appeared correct after rehiding/setting menus. But now I am seeing two 'courses' menu in admin, one was real for custom courses post type, one was fake leading to 'posts' menu in fact. Means 'Posts' menu was renamed to 'courses'.
Further I installed 'bbpress' plugin which created custom posts types and menu for forums, topics and replies. Again menus are misaligned so I reset again the custom admin menu. Now, I have two 'replies' menu in admin, one real for 'replies' post type and one was linking to 'posts' menu, means 'posts' menu is renamed to 'replies' now.
The result which I seen is that default 'posts' menu is renamed automatically to any custom post type available most likely to the recent one. I even tried to set the custom text in ag-custom-admin 'posts' menu text, but not working. Admin still not showing real 'Posts' menu text, although the link on extra 'courses' or 'replies' menu are correct and taking to 'posts' correctly.
All above issue in menu text is for non-admin. For super admin the menu items are correct as there custom menu not applied by ag-custom-admin.
The reason I suppose to be the link for 'posts' menu is http://site/wp-admin/edit.php and for custom post types is like http://site/wp-admin/edit.php?post_type=courses and http://site/wp-admin/edit.php?post_type=reply
Here you can see the default 'posts' has no argument, and most probably ag-custom-admin is using url arguments or slug in some way to set text, and since for posts no slug is available so its taking the most recent courses or reply slug/argument available and showing the wrong text. So, this plugin need the empty argument check I think to fix the issue.
Also, the mis-alignment of menu items after adding new menu items should also some way to be fixed in plugin, because it is very awkward to set again all menu if in future a single feature/custom post type developed/added in the site.
I hope all is clear now, please let me know if some doubt. And please try to fix the issues asap.