Images and graphics in PDF turn black upon upload onto a website

Hi there!
I have a problem with a pdf file that I have uploaded onto a website in the process of creating a self published book. It appears fine when I view it as a pdf prior to upload but, once I upload it, some of the images are replaced by black boxes. This seems to be the case no matter what browser is used. Any ideas of the cause or how this can be fixed? the pdf is a compilation of a number of student pdf's that I combined into one so, I don't have the original files used to create the pdf (in design, etc).
thanks for any advice or help that you can offer

Here is an example PDF, I had to take a screen shot so I could clear out the customer data. This is before we upload it to the investors website. Keep in mind this is a single page out of hundreds that look fine.
http://imgur.com/4dKQt1H
This is the after shot. The "fannie mae" logo is "blacked out."
http://imgur.com/ved34Om

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Images and graphics in PDF turn black upon upload onto a website

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