Part of logo missing when exporting to PDF

I'm running ID CS6 and Acrobat Pro X.
When I export a document as a PRINT or INTERACTIVE pdf, part of my logo goes missing. The funny thing is that our design team are all running the same programs and 3 of our members can view the logo completely, the other 4 see half of the logo missing, I can see the logo just fine.
• The logo mark is visible, but the typography that is part of the logo is missing?! And it's a single grouped object in Illustrator.
• We've compared the settings on our teams' programs and on my ID program as well, and nothing seems be remotely related to the issue.
• Finder on Mac shows mixed visibility in file preview on different computers. Some show, some don't.
• In the past, I've been able to place vector objects from Illustrator into Indesign completely fine. I prefer vector over image because it allows me scaling flexibility.
• I have not changed any settings on my program between the time I was able and not able to do this. I don't understand why different people are getting different results on their screens. And in a couple of occasions, it has happened to one of our team members and it fixed itself mysteriously.
I would like to provide screen shots, but it is a private design.
One key note to realize is that the logo is completely outlined and grouped as a single object. I then save the logo into the same folder as the ID file (tried both, .EPS and .AI) and placed it (CMD+D) into InDesign. Both files are CMYK files.
I then make my PDF by hitting (CMD+E) to export, choose PDF Print. On the PDF settings, I choose [High Quality Print], compatible with Acrobat 5 and beyond, uncheck optimize for web, include bleeds, no color conversion.
I've had issues in the past where hidden layers in an .AI are still visible in the PDF. The .AI is imported into InDesign then exported as PDF... The hidden layers from the .AI preview in Finder, but then vanish when opening the PDF...so buggy.
Make any sense?!...

Similar to Mikey's response… If the logo has a spot color in it and it overlaps any raster image (or vice versa), then the overlapping part will appear white if "Overprint Preview" is turned off in Acrobat. This is really a bug. One possible fix is to export the PDF as an PDF/X-4:2010 in the "Standard" drop down—this preserves all transparency layering without flattening.
This issue causes frequent headaches and confusion in my workplace, especially since a lot of people want/need to hold on to the PDF/X-1a standard, which flattens the artwork.

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