Hey Stainer,
I ran into the same problem a while back. What i did to fix it was follow the directions that the teacher gives on where to go to get your certificates. So if you go to class hall in Varanas and talk to Listi Pursdon, ask him How to Obtain a Training Cartificate. He tells you all the different places to go to get each certificate for each level you've reached. Follow this and you shouldnt have any issues. Its a bit more of a pain in the arse, but it works.