I have Acrobat pro xi version 11.0.5. We have headers with a graphic and text on top of the graphic. If pages are combined, the text in the header disappears. Actually what is happening is the text will go behind the graphic. I tried bringing the text forward and moving the graphic back, with no help. This is an issue with 11, because version 10 works fine.
Is the original document a Word Document? if yes then what is version of Microsoft Word?
Which Operating System?
Try printing the document to Adobe PDF Printer and then check the issue.