Hi. I'm having exactly the same issue converting some PDF's to epub format for the Sony PRS600, I've been resorting to SIGIL to try and correct this and other issues recently.
It's also doing other strange things to the format of some of my pdfs, I'm not sure if it's something that's come along in the latest version, I've been using it to convert PDF's to epub for about six months now and I'm having quite a few wierd issues with my latest batch of conversions.
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