What vanes are you using with his arrows? Read the directions. Some vanes you need to clean the bases to get the oils off. How old and what type of glue? Just my opinion, but I don't like the Crazy glues. I like Fletchtite Platinum.

Sounds like you're cleaning the shafts OK and with the right cleaner. Although I've never used the fletching jig you have, if the vanes are making good contact with the shaft what jig used shouldn't pose a problem.