I have this issue all the time, or atleast something similiar. It has to do with extra fields.
Say you create a category called "Dollars", then under it you have "Liberty Seated Dollars" and a bunch of other categories. If you add extra fields to "Dollars", and tell it to go to all child categories, it won't, until you go add a new field to 'Liberty Seated Dollars'.
|_ SUB CAT
Add extra to main cat, then tell it to go to children. SUB CAT won't have MAIN CAT extra fields until you add one to SUB CAT, then they all show up.
My gallery is huge, I know this is an issue because if you look at the size of my gallery, you'll see there are hundreds of categories. It's extremely annoying. Extra categories in PP is NOT movable either...otherwise you'll lose the data.