I just realized that I gave you incorrect instructions if you are running iOS 5 as your profile line indicates.
If you are running iOS 5, you close apps like this.
Tap the home button once. Then tap the home button twice and the recents tray will appear at the bottom of the screen. Tap and hold down on any app icon until it begins to wiggle. Tap the minus ➖ sign in the upper left corner of the app that you want to close. Tap the home button twice.
If you are running iOS 7 and my instructions did not help, the only thing that I can suggest is to manually root through all of your emails - or do a search in the mail app.
Go to the Inbox of your email account and type Flagged in the search field and see what that turns up. If you really do have flagged emails on the iPad, that should find them for you. It works for me that way.