What is the bit rate/depth your project is at? Export as the same. Put that mix file into the project lined up and muted. Now switch between the project and mix file. Are there any differneces now? If so, something is screwy in the export process. X1 has been inserting new tracks for me routed to the interface output.
If the mix sounds fine than there is something going on in the conversion rate. See if doing it via two steps (export and then convert) works better.
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