After a tone more debug a got a lead when I noticed that disabling -Dorg.icepdf.core.scaleImage=false the fax capture started showing the all the images in the resulting TIFF. It turns out the stream class does it's own image scaling if the images in question is not a mask or smask. The Shapes class was also doing scaling of all images types bing added to the shapes vector. I couldn't find a reason as to why the image scaling was causing the print issue, the images where being painted but just not showing up. There was no clipping in play here as well. The only think I can assume is that something odd was happing with the image processing during the print as screen was ok. The images in question had a mask property which might further complicate things.
The fix as it stands is to remove the double scaling. If there is still problems then it is possible to disable scaling all together with -Dorg.icepdf.core.scaleImage=false.
I can only reproduce this using JDK 1.5 and not 1.6. One strange aspect of the PDF is that there are very few clips defined. I'll look more closely to see if the memory manager is cleaning up earlier then it should.