I just had this issue in AI and it was because one of my artboards had mixed color profiles. I had copied something in from InDesign and it had some spot colors. Even though I rasterized that whole artboard in AI, when I exported to PDF it didn't want to show anything but the spot colors (I'm guessing because I had "preserve spot colors" enabled when I exported). I converted the spot colors to RGB and everything showed correctly after I exported to PDF again. Not sure if it was just my specific issue, but figured I'd add my issue here just in case it helps someone else.
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