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This is a known issue. We have just upgraded to matplotlib 1.0.0 in Sage-4.6.alpha0 (a prelease version), and there are some open tickets related to this. Essentially, matplotlib didn't allow specifying pixel width and pixel aspect ratio and a sort of anti-aliasing and a few other things all at once, at least not the way we were using it...

But essentially it's hard to ensure this kind of thing won't happen without breaking certain other things, due to the vagaries of computer graphics, apparently. See for the issue itself.

I think this should answer your question, though perhaps not satisfactorily :( please feel free to comment on any of the Trac tickets with comments that will help us make it more perfect - especially with which of 1-3 you prefer in the ticket.