it sounds as if the item is in a pending state. Have you got After Backup set on the Vault Store? What this would mean is the item will not be removed from Exchange until the backup of the item has taken place in EV storage.
Open the Vault Admin Console, browse down to your Vault Store, under vault store groups etc. On the General TAB fo the properties check the settings option. If set to after backup this will be the reason.
You will need to reset the archiving attribute of the data within the storage area (partition). Most backup software does this or you can use the attrib command.