in the Adafruit_BBIO/Encoder.py description section
is the second pin of the eQEP0 wrong set

here the wrong lines

======= ======= ======= ===================================================
Channel Pin A Pin B Notes
======= ======= ======= ===================================================
eQEP0 P9.27 P9.92

I think the correct header pin number is the P9.42. After check the schematic of the BBB Rev:C, this connection is the only one on the board that traverse the eQEP0_INB to the outside world.

Regards Ronald