I'm having the exact same issue. I wonder if anyone has figured out a solution to this problem.

Same experience I'm having. I think I must be overlooking something though. When I go back to My Music I see it all and they are all checked as shared though when I click on the ones that don't show in the invite account it says they are selected to share but no one has been invited. I would have thought that sending an invite at the root folder would have done it. I'm a bit perplexed - surely I don't need to go in and individually invite for each folder. I'm sort of thinking I may have sent out that initial invite before all the sub folders were indexed or something. I don't know how I should backtrack to catch them all. Maybe I should send another invite for folder? A bit perplexing.

I've tried that, it doesn't help. I even wiped the drive and did a fresh start with a new folder and it did the same thing. I then theorized that maybe it didn't like seeing "&" in the sub folder names so changed them to "and" - that didn't help.

The thing I'm going to try next is to start with a totally empty disk and populate the folder via the pogo upload tool. Up until now I've been build the contents with a bulk copy as a regular USB drive outside of the Pogo.

It would really help if there was a document of some simple rules that especially covered things 'not to do'.

Try changing the Sort.  When i changed it from default it seemed to show more pages. Very strange but that was the work around i found.