I recently edited my organization's intranet site by creating a JavaScript file which utilizes jQuery v.8 and jQuery UI. My custom JS creates an unordered list with site navigation that has drop downs to sublinks with jQuery animations. The reason for this instead of SharePoints navigation tag is because our intranet has tons of masterpages, so instead of having to change each and every masterpage when a new link is added, you only add it to the JS and since each masterpage is referencing my custom JS file, the navigation will be created.
My problem is, after implementing this, certain users who used to have access to a subsite reserved for managers no longer have direct access. Strangely though, when the Access Denied.aspx page is displayed, there is a link to go back to the Site, and when clicked will take the user to the correct spot in the subsite. Users with Full Control have no problem accessing the site through the menu. Most of the user's for this subsite are stored in Active Directory groups, and those AD groups are assigned permissions. The AD groups assigned are given Limited Access.
In my custom masterpage template, I deleted the old SharePoint tag for navigation and inserted a blank div tag with which my JS uses to create the navigation. This div tag is not placed in the same spot as the old SharePoint tag, but a little higher up, right before div with class of "s4-lp s4-toplinks"
Just wondering if anyone had any ideas with regards to permissions and custom navigation menus. For legal reasons I cannot show code, but I can explain the best I can if anyone should ask.
Thanks