I'm having the same problem. Is there a page limit? I started having the problem after passing 300 pages created.
The pages are there and accessible to view, just not from header area or the tabs that usually appear after clicking on the text in the header area.
In trying to figure this out, I've discovered that creating a new page appears to reset everything to work quickly for a few minutes and then it reverts back. It will also work properly for a few minutes if you update a page. Pages that were disappearing last night now have no problems after about 9:35 this morning but new pages have the problems.
To experiment I've added the page with url below as a parent which should show up directly in the header bar and doesn't but can be seen if you go straight to the url: http://hikingangelesforest.com/htest/
I also added a page "another test" as a child to the parent "references". I added a link to the page on the references page and it can be viewed by clicking on that link see: http://hikingangelesforest.com/references/ The three other child links shown in the above url show up when one places a cursor over the "references" text in the header area. The new child page "another test" does not.
I don't know if this is related, but I am receiving a significant increase of spam right now. A lot of them are making it past akismet (easily over 50). The problem with the pages also started on the same day with the increased spam.