There’s neither GPIO060 nor GPIO_60. Instead there’re four GPIO subsystems [0-3] each one controlling 32 lines [0-31].
Both pins (P9_12 on BBB, P2_08 on Pocket) are connected to CPU ball 0x1E, and that’s controlling line 28 on GPIO-1 subsytsem in GPIO mode. There’s no hardware difference.
Which code do you use to toggle the GPIO? (Did you try libpruio?)