For what it is worth...

I had this problem occur a while back; In my case it was coincident to installing/using a DNN5 skin in place of a DNN4 skin, though it turned out NOT to be a skin problem...

My TABS tables (pages) had 'bizarre' numbers in the 'level' column and 'order' column.

Some skins (maybe modules?) ignore pages (Tabs table in db) with page levels not in the range of 0, 1, 2, 3.  This table also controls visibility, parentage, order (odd numbers only??), etc.

I found negative numbers, 4-and 5-digit numbers, numbers larger than 3 and non-contiguous numbers throughout my Tabs table as levels, and equally wierd entries for 'order'.  With coaching I had to fix it manually and it has worked fine since.  Only a suspicion how it got hosed to begin with.  DNN5 and a new DNN5 skin couldn't deal with the anarchy in those legacy tables but DNN4 and skins before DNN5 didn't seem to care...  :)

Bob