Which folders is the email showing in? Are you confusing the MESSAGES folder and the
email inbox? If that is the case, that's how it works - one message in the
email inbox and a pointer to that message from the MESSAGES folder. There's no way around that, except to hide one of the folders.
The SEPARATE option separates SMS/MMS messages from the EMAIL MESSAGES by creating another icon for SMS/MMS and putting those TEXT messages there.
Juwaack: the option can
be theme controlled, but you can override that setting by selecting the value for the SMS and Email Inboxes: option in MESSAGES/OPTIONS/GENERAL OPTIONS.