Chances are you are just viewing your Inbox instead of your account.
Open Mail, and with your iPad in landscape view tap on the Mailbox button at the top left.
You should see two lists, one for Inboxes and one for accounts. If you choose the Inbox that is all you will see. If you choose the account you will see all the folders that are synced with the account.
If that is not the problem, then my recomendations is to delete your account and re-add in Settings >> Mail, Contacts, Calendars. That should force all folders to resync.