We have WHMCS v4.2 setup with two departments sales@ and support@ , also under General -> Mail we setup server@ on an SMTP configuration as we're using google apps for all our emails.
Receiving notification of a new ticket, getting tickets from customers emailing us, and being able to reply to them in whmcs works fine.
The problem is when any department replies to a ticket, the emails are sent with server@ being the reply-to address, we need the reply-to to be the department that handled the ticket, meaning if its a sales ticket a customer needs to have sales@ be the reply address when they click reply, likewise if its support, then support@ , not server@