I have had similar problems with PAF5 where one or more 'lists' suddenly become truncated. This happened recently with the list of individuals [click on the individuals tab]. When viewed in RIN order all 1088 individuals were shown but if I clicked on the Full Name tab [names in alphabetical order] the list ended after a couple of 'A' surnames. The missing individuals were still there in the family and pedigree views.
I managed to repair the file by exporting as a .ged file then re-importing into a new file. Perhaps this process regenerates the lists?
Hope this works for you. Has anyone else come across this problem and identified another fix?