Can you share this a PDF created using PDF producer by Quark, never used it hence would like to check...
Also it will be better if you post your query on Indesign forums as it seems to be INdesign specific stuff.
Ok..Goy your file..
When exporting the file to PDF from Indesign,
In the "Export PDF" dailog box :-
In the Compression options ,(on the left)
change "bicubic downsample" to "Do not downsample" for all and then check , it will be good to go.
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Manish asked me to look into this, but I'm not sure how much I can add. The main problem I've seen with PDFs produced by Quark has been the inclusion of OPI comments (I stopped upgrading Q at version 6, so I don't know if it's still true, but it used to be that OPI was enabled by default in Quark). That would commonly cause images in the PDF to disappear. Your case sounds different, though.
I might have some time later today to take a look (I know Manish has already looked at the files) if you want to send them to me.