Thanks for the feedback. Is the incomplete list only with files on your Pogoplu-enabled Mac?
When using the web interface to settup an active copy, the folder list diplayed is incomplete.
In my situation, I was trying to create an active sync between a folder inside my Documents folder (on Mac OS) and a disk attached to my pogoplug.
The folder I wanted to sync was not in the list, but "creating" a folder with the same name as the existing one, put me in the existing folder, where I finally have been able to finish the active sync setup.
Indeed, the problem only happen with my mac "Documents" folder.
The problem happen within the "Microsoft User Data" which is always the last folder displayed by pogoplug. Trying to browse this folder within the web GUI bring a "This drive is not available." message.
I am also having that problem on my iMac. In my pictures folder ... only the three folders are showing up ... but not any of the files that are not in sub-folders.

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Indeed, the file list is also incomplete in the "Files" view.