Refunding a ticket that was (part-)paid with a voucher has always been tricky. I did this again recently and managed to get the website to finally accept the refund request after much coaxing.
I got a response a few days later saying that as I had booked the ticket using a travel agent I would have to deal with the agent. I had booked direct with AFKL though the voucher used initially to book had resulted from an earlier cancellation of an Opodo ticket.
A call to the help desk got it sorted instantly.