Parts of my white logo disappear when viewing seps in Acrobat - Urgent

Hi folks
I have been supplied with an .eps logo that is comprised of various grouped elements all on one layer. All the fills are set to C=0 M=0 Y=0 K=0. I am using Illustrator CS
I have placed the file in an InDesign CS2 document against a coloured CMYK background. The logo looks exactly as I would expect with the white parts showing. If I output a PDF it looks correct. If however I view separations in Acrobat and InDesign parts of the logo become invisible.
What is happening? I have examined the logo and cannot see what would cause some parts to disappear. I have not yet heard from my client whether the final printed output is OK or whether it's a disaster.
Thanks in advance for any clues

Further to this...
I have opened the PDF into Illustrator CS and the logo shows correctly. However if I select the parts that disappear in the seps view mentioned above, the CMY values are showing as all zero apart from K which has become K=0.1
The rest of the logo is showing K=0. Looking back at just the logo in Illustrator shows that all parts of the logo are with a zero value.
Even so, why would those parts then disappear - and what could cause some parts of the logo to have K=0.1?? Very odd.

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