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9199653
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reproduced with Inkscape 0.47+devel r9440 on OS X 10.5.8
The images in the exported PDF are not missing but appear to be incorrectly (?) scaled.
The problem does not seem to be using inverted B&W images as masks per se, but related to the preserved (nested) transformation(s) applied to the parent group of the masked rectangle (scale and translate to correct position in the page layout) and the masked rectangle itself (vertically flipped): If - before exporting to PDF - I ungroup and regroup that innermost group again (so that the parent transformation matrix is combined with the 'flipping' matrix of the masked rectangle itself), the image is rendered correctly scaled in the PDF file - but is strongly pixelated.