Just a guess, but it could be something in the kernel that has been compiled into Raspbian but not into OSMC. Perhaps @sam_nazarko might have an idea and it wouldn’t hurt asking the people at element14.
There is also a gpio utility that might be of use in determining the state of the GPIO pins, which could be of use. See [SOLVED] RPI.GPIO won't work after fresh install - #3 by dillthedog