I think the PDF Viewer works by extracting the images and text and displaying them using the standard rules of HTML and CSS. If the problem images are JPEGs, you could be running into a color management issue, but first, do you still have the source images that were embedded in the PDF? Could you check on whether those have the same problem when you view them in Firefox, or whether the problem was introduced by the viewer decoding the PDF?

It's actually not the images in this case, but font and object colors (by objects, I mean shapes that were drawn in Adobe InDesign). The file renders correctly in Adobe Reader.

We've exceeded my knowledge of the viewer's internals. Has the report been posted for viewing or is it still in process? If it's not public, can you create a one page demo that exhibits the same problems? I think that might be helpful for troubleshooting.

Sorry, that would have been helpful to begin with :)

The PDF in question can be found here: http://www.simpsonhousing.org/annualreport.html

The link is at the top of the page, under "Annual Report 2012." However, all of the PDFs listed on the site are displaying incorrectly, not just this one!

After looking at this for quite a while, I have to admit I do not understand how the viewer works...

I did notice on page 5 that one of the blue rectangles is the correct color. If you examine your source document, can you see any reason why that might be?

No reason any of the graphic elements should render differently, that's why it's so frustrating. All of the rectangles are the same color value and were created the same way in the source document.