Generally, reports will only show the default photos, but I assume that is what you want. Check and see if the photos that don't print will display in PAF. Basically, if PAF can find the photos to display them, it should find them to print them.
If you have a PDF printer driver (e.g. the one that comes with the free version of PAF Companion), set it as the default printer and try printing to it (remove the check mark at Print-to-file). What happens? Do you get the photos printed in the pdf document?
Uninstalling and reinstalling PAF might solve the problem. If uninstalling, make sure you have copied any data from the PAF5 folder. I don't believe it is deleted during an uninstall, but I would hate to be wrong on that point.