All the other labels are correct and synced according to their various settings. There is no particular setting for "All Mail"
Today, I only see up to August 28. When I scroll to the bottom it adds older messages as expected.
Tommorrow, it will add August 29's email to the All Mail Folder. It's been doing this ever since I got the Nexus 7.
I have no problems on a Samsung Galaxy Note (same account, but obviously running ICS and not JB). When I have already filed everything, I can go to All Mail and see the messages which recently came in, regardless of their labels.
This behavior is not happening on a Google Apps Domain account in the same Nexus but is happening on a gmail account