Are the logos set in spot colors? Default acrobat settings don't show spot colors, but this can be changed.
I don't remember the details, but I'll check it out and post back
EDIT: I can't reproduce the problem in my current version of Acrobat, but I have run into this in the past, and it was a preference setting in Acrobat that fixed it. Would you be willing to share the PDF file on Dropbox (or some other file sharing service), so others here can see if they have the same result?
Second edit: I misread you post - still, sharing the PDF may help someone here track down the issue.