Try going to the iCloud settings and turning Mail off. Visit the mail app to make sure your iCloud account is gone, then go back and turn it on again.
If that does not work try signing completely out of the iCloud account. When it asks if you want to delete the local calendars, contacts, whatever say yes (to help prevent duplicates. I again suggest visiting all the affected apps all the apps to force them to clean, then sign back on in iCloud settings.
I'm hopping this will force the iPad to reset your email to what's in iCloud.
One caution. If you have apps that are using Documents and Data in iCloud it would be best to make sure you've got good copies. I've never lost anything critical when starting/stopping this service, but I have had duplicates and other minor hitches that make me wary; especially in the iWorks apps.
You can also try it from the other end. Uncheck the alias box(s) and exit the preferences (to force a save), then go back in and re-check the box. This is simpler, so you might want to try it first. {I always seem to think of the easy stuff last, hmmm}
That's all I can think of for now.
Good Luck.