I have a POP email account. My iPHone 4 use to only pull up unopened, unread emails, which is what I prefer. The iPhone 5 now pulls up all emails, even if I have read and deleted from on my laptop.
Use imap on both the computer & device, that way anything deleted on one will be deleted on the other when you access you mail account.
I had the same problem using pop server, the delete from server function stopped working due to isp changing to Google servers.
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