when doing a Save As Pdf check the settings in the dialog box, compare to someone who doesn't experience your issue.
only other hint I can think of is something about setting Overprint but that is something I heard of when working in a different program altogether.
Have you tried printing .pdf instead of saving? Is there a difference regarding your logo?
I've found that when you have a drawing view close to the title block, and the bounding box of that view extends over an image in the title block, you get this result.
The only consistent way around this issue is to move the offending view.