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This is still happening with Inkscape 0.48.4 on Ubuntu 14.04.
My case is I'm opening bank statement PDFs in Inkscape. They look fine in Inkscape, but when I save as PDF or print to a PDF file, the images (bank's logo, next page icon, etc.) don't appear and black squares or gradients appear in their place.
The workaround is much as in comments 5 and 6: select an image, ungroup, select again, right click > Release Mask. The image inverts, so Extensions > Raster > Negate. This leaves faint black outlines but at least the images appear in the PDF.
FWIW the originating PDF is generated by Author: TrilliCom LLC, Producer: TRCA2P14 V1.39C (and some poor drone at the bank fiddling around with its logos until the original PDF looked OK).