Hi,
Did you check the persona log file? Is there anything like 'aborting sync / upload' message in the log file?
If you save a file on the desktop, is the file replicated to the persona repository? Did you re-check your NTFS-permissions on the share?
I had another case where a folder was not accessible and caused the profile sync to be incomplete, e.g. some folders were synced and some were not. I crawled through the persona log file and finally catched a folder which I later added to the excluded folder GPO. After that the sync was complete and I never had issues
Regards