Hi,
yes, it should show 1,2... etc if there is unread mail. If it's not, there is a bug... Can you tell us if its always 0? What is mail account server? We tested with gmail and couple other free and commercial mail account services and it worked fine.
We provide our own plugins set with roundcube, that integrates epesi with roundcube (archive, addressbook, autologin etc). We also use our custom config file and modified template.
You shouldn't care about two copies of the same script, it's pretty small.
Cheers,
Paul