There is a catch when Setting up and configuring the command notification subscription.
If a command is not getting executed first things to test are:
1. Notification Account under Administration -> profiles. See what account is configured for the Management Server under which the command does not run. Then run the exe or script under this account to see if it works manually. If no account is configured here, the default action account will be used instead.
2. If manually running the command works, it usually means that the command is getting executed elsewhere. So go to the all notification resource pool -> manual membership and put only the MS where the command does not get executed. This is the only way to force a command on a specific MS. Otherwise all Management servers will be sorted out and the first one, will be picked to run the notifications. This is in order to enable high availability for the notification pool.
Also, the only supported scenario is that all MS are equal/ have the same updates, software etc.. that the commands can use regardless of the MS.
Otherwise the only way around this is to leave 1 MS in the pool.
PS: The RMS emulator role does not have any impact on notifications, it does not affect the sorting at all. Only Management Packs like Exchange 2010 depend on this.