Mavericks and Yosemite marks mails in multiple accounts as read
Strictly speaking, You have read it.

I've noticed recently that if I get duplicate emails to 2 accounts, Mail is actually appearing to merge them into one email [at a user-level anyway, idk about behind the scenes]

I know of no way round this, so maybe try using Flags instead of the 'read' indicator. More work, but more reliable.