I brought up this issue when Bela first came out, and I tried to resolve it with no success. (and if I had resolved it, the fix would go away with subsequent updates.) Anyway, the eQEP encoder inputs aren't activated, which I believe is just an issue of enabling them in the kernel config when compiling. Is this something that could happen? I don't think it would detract from the current functions of the Bela board in terms of pinouts.