One of the website that I manage the menu system is not working. I have installed many modules (including the commerce modules) and are not being displayed on the menu. However, all modules links (and commerce) works, if I type it on the URL.

After troubleshooting a little bit more I figure out that this is not only for commerce. I created a new content type and is not been display on the node/add page or in the admin_menu. And once again I'm able to go to the page if I type the URL.

I click on rebuild menu, I flush all caches and still not been register. I do not see any Drupal logs errors.

How can I address this problem ? I cannot expect the sysadmin to know all the URL.

Update 3/27/2015

I'm now using the latest Drupal (v7.35) and I noticed this at first on 7.34.

Like I mentioned before it is not only on the menu. So I do not think the admin_menu is the problem. I remove the module admin_menu and use the toolbar module. But there are missing links on the pages that are been created for the latest module that I have installed. So any module that I enable from now on it would not register the pages.

Update 4/3/2015

I'm now using the latest Drupal (v7.36) and I noticed this at first on 7.34.

I disable/uninstall and enable drupal core menu module and still not fix this issue. Someone from the Google + community suggested that this issue may be cause by the jquery updated I try to used different jQuery version and still have issues. In addition, I try to follow this How to completely wipe and rebuild drupal menus? and to rebuild all my menu and did not work.

I strongly believe is need to be something with the hook_menu not working on my Drupal website.

Update 4/4/2015

I notice that if I add a new content type it would not appear the links on the node/add nor under the content menu. However, it appear in the page admin/structure/types and in the menu under structure -- > Content Type.

Some more updates to address one of the suggested answers to try to get my issue reolved: