There is a bug in 5.1 on El Capitan that was causing duplicating custom command sets to crash Rhino for Mac. We worked on solving this bug before release and were unable to. We are still working on it. We decided that - rather than have 5.1 on El Capitan crash - we would release it with the Duplicate button disabled. This was a “lesser of two evils” decision.
The good news is: when we do manage to fix the crash bug, working with customizing command sets on El Capitan will go MUCH faster than it did on Yosemite. Cold comfort, I know.
We will release a fix for this in an update as soon as possible.