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bbfa235
(Get the code!)
Just wanted to add that I am also having this problem and that it never happened to me with inkscape 0.46. With 0.47 some areas of the same image are blurred and/or disappear when exporting to EPS, PS, or PDF.
Tried inkscape 0.47 on Ubuntu 9.10 and Mac OS X 10.6, same exactly problem persists. Also tried with the latest nightly build of 0.47 (trunk) compiled on Ubuntu 9.10 -- same thing.
Very annoying. I am pretty sure none of the layers were rasterized before when I exported to EPS using inkscape 0.46 but I'll have to check and it's not easy since I no longer have 0.46 installed on any of my computers. The image in question was originally created in Mac OS X version of Illustrator and has plenty of transparent layers...