I am having similar issues with the whole DNN page hierarchy system.  I thought it was my sites till I tested it pretty thoroughly with a clean install of DNN 5.4.2.  Even in these clean installs using the default skin, creating pages and putting them in a hierarchy can cause errors - that make this a very difficult problem in using DNN in a production environment. 

Here are some of the things that have happened to me:

1. In the Admin/Pages module, pages created in a nested hierarchy sometimes do not display with ellipses in that management interface, even though they appear in the menu as a sub-menu correctly (interestingly however, these pages display as root pages on the default bottom menu!)  EXAMPLE HERE
2. When trying to assign a hierarchy while the page is being created, the full page structure is not shown in the drop down control (where you choose the parent page).  Sometimes only the Admin menu is displayed; sometime just a few of the main menu nodes (often with some main nodes missing).  It's so variable what happens in this drop down when it gets confused.
3. When the system gets really screwed up, the Admin/Pages editor will not allow the moving around of pages and will not promote or demote nested pages. VIDEO HERE
4. When this happens, the main menu bar will display the submenu name instead of the root name for a main node.  The submenu node also displays as a top level node on the main menu bar!  EXAMPLE HERE
5. When it gets this badly screwed up, adding another submenu node will actually delete other submenu items!  I am not joking.  This is in an otherwise clean install and it is even more disturbing in a production website.

I have reported this to the core team and was told basically that it didn't concern them until it was completely reproducible.  I'll try again and hope not to get flamed this time.
Peter Smith