As Eugene suggests, it looks like it could be an overprint issue of some sort. I think the Ghent specs allow, but don't require, either live transparency or flattening, so it will help us if you can tell us exactly what settings were used, again as Eugene has requested, and whether there are any spot colors in the file, and where they are, along with any information regarding transparency or overprinting that is built into the .ai file. A screen capture of the file in illustrator may help, too, for us to understand what it looks like.
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