I am aware of that, but there is also a setting that addresses syncing email.
If you are looking at what I think you are, then read the text at the bottom of the box. It should tell you that this setting only syncs you email account settings, not the actual email messages. I don't recommend turning this on. It's rarely worth the potential confusion.
To get the messages you still have to set the account up on the iPad under Settings > Mail, Contacts, Calendars, Add Account.
If that account is a POP account, then the behavior you've described is typical. Depending on how a POP account is set up the iPad may not be able to actually delete emails on the server. You'd have to check your account set up on the server. Be ware though that if the iPad does start deleting these emails, it will do so on download (most likely), which means your computer may never see them, even if you don't manually delete them.
POP accounts don't work well with multiple devices accessing them.
If you email provider offers IMAP or Exchange as an alternate way to access your email, you'd be better off setting up that way, both on the iPad and computer.
