I can't test anything since you put your site offline.
But it's clear that you have Itemid problems. Make sure that section (articles) has been added to menu and it's public.

I think I have fixed my problem.  Let me see if I understand the reason why my fix works though.

I simply added a "list content section" menu item under a "special" menu for the section I was having problems with  (as you kind of mentioned in your FAQ).  In my case I added the "articles" section.

Does this work now because there is now a link in the directory table which didn't exist before that your program can find when traversing the directory table?

All of my article content were and still are referenced thru com_alphacontent which we know is a problem.  Presumably the content id could not be found previously because there weren't u&able links to&from the content to the menu data table.  Which I gather is where all of your traversals to find ids start.

Perhaps in that case it would always be advantageous to do what I mentioned with all sections or equivalently just make the added "link content section" menu items unpublished.

Thanks Emir.  Bob