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The problem is in our Polygon class - somehow it's not saving correctly. Compare these.

sage: polygon([(0,0), (1,1), (0,1)],alpha=.1).save('test.pdf')
sage: polygon([(0,0), (1,1), (0,1)],alpha=.1).save('test.eps')

If I can narrow it down a little more, I'll open a ticket. It's conceivable that it's a matplotlib issue, but I'd guess it's ours first.