Yes, Microsoft's keyboard connector changed between the Surface RT and Surface Pro to add additional pins for power.
This is why Microsoft's latest Power Cover also doesn't work on the Surface RT but works on the rest.
It is possible the Music Cover takes advantage of the additional pins.
I generally don't like to give MS the benefit of the doubt, but in this case I know a lot of work went into the keyboard cover between the 1st gen (both pro and RT) and 2nd gen surface units. Is it possible that the connector has changed?