Overlap Madness

I've been twiddling with this file for days now, and for some reason,  the areas are still overlapping--the region-before isn't showing up  correctly on page 1, not at all on page 2, and shouldn't be displayed  on pp. 3-4 because they have no content (how do I suppress the header?)  Page 1 is missing the footer. And, strangest of all, the page basically  shows up with areas not overlapping when I run it through the AltSoft  checker. Something FOP isn't doing right?

       
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