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Actually, the problem is with Mathematica's export, at least with Version 10. I have been saving a file wit MatrixPlot (using Save As...-> PDF), and have encountered the same problem. Turns out, MatrixPlot (and similar) data is being exported as a bitmap, which gets blurred in Adobe Reader 9 (which I have), even if "Smooth line art" and "Smooth images" is ...

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