I've spent some time on this issue looking through similar issues and documentation and cannot seem to shake this problem with this specific PDF. There's some images in this PDF that have a DeviceCMYK color space and they don't output correctly. I've inspected the PDF in iText Rups in the hopes of finding something useful. I suspected this was a transparency issue, however I cannot seem to find any reference to a second bitmap that'd be the mask layer. With that said, I'm unfamiliar with how this PDF was formed as it was one given to me from a colleague to test with.
I've tested using a PDF containing a CMYK JPEG found online with a color space of ICCBased and it works fine when being read and extracted to file or compressed. There is obviously something being missed in our PDF image extraction process, whether its a masking layer or an ICC profile i'm not sure. My efforts to debug this have not yielded a lot of helpful information, however I was hoping someone could point me in the right direction with their experience with this issue.
Note: I'm using the ImageIO Plugin TwelveMonkeys to allow support for CMYK JPEG images.
The below images are a screen-grab of the image as it appears in the PDF. The second is the output when extracted using iText 5.
EDIT: updated the second (dark version) image to be the jpeg produced after extracting from the PDF and not a PNG file. Have also added a screenshot of the PDF inspector for the page containing the example image.