CS5 file printing at 50% opacity, even though all layers are at 100% opacity! HELP

Hi,
I'm having some SERIOUS issues with InDesign at the moment. I'm quite well versed with the program, and have never encountered this issue before - I am at a loss at what to do or how to fix it.
I've been designing a magazine layout for a University assignment - the file/template was downloaded from the Uni website, and had 1 existing layer which we could not alter. I've then added a number of other layers of images, text, shapes etc. Some which have various drop shadows and effects on top.
When I went to test print the layout, I noticed that it was though it had been set at 50% opacity - everything was see through and I could see multiple layers of colours. I thought that I had perhaps accidentally mucked with the settings, but after double checking, I was baffled. Originally I had exported it as a high quality PDF file, so I then tried printing it as a CS5 file straight from my mac - I got the same result. I've since tried both the PDF and .idml files on both mac and pc, but nothing seems to change.
The odd thing is, on my screen, both PDF and .idml files are at 100% opacity and vibrant blocks of colour - I am quite confident that the settings on the layers are all at 100%, but I still cannot seem to fix it.
Some advice or answers would be extremely valuable! I have the chance to resubmit, so I'd like to know how to fix it, if possible!
Thanks

I'm not really sure what to show you.
In overprint view it looks wrong - 50% opacity - i think we're on the right track!
That's it in overprint view (above)
That's how it's supposed to look - I'm not sure if you can see the difference though, it's not very clear.

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CS5 file printing at 50% opacity, even though all layers are at 100% opacity! HELP

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