You say "all my accounts" implying you have more than one. You suggest that you have all your accounts "hooked up to the iPad" but the iPad has multiple InBoxes - one for each account. It's possible, from within the iPad's Mail app, to consolidate all the InBoxes into a single unified one, but it's equally possible for them to be separate.
So, the emails that you don't see - are they from another account and hence, possibly, another InBox?
Tim