I don't know if my experience with a different file is related or not, but you might try my "solution".
I have a PDF, from the Internet Archive, that displayed fine on my PC in Acrobat Reader but displayed blank pages with the occasional image when viewed on my Kindle 3. I "fixed" the file by printing from Acrobat Reader using the PrimoPDF printer driver which creates a PDF file.
The printing took a long time, ~15 sec / page for 175 pages just to spool the file and about as long for PrimoPDF to create the output file. The results were fine and view properly on my K3.
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