simple problem, stupid design issue (that has not been fixed since the first MRF's). Once any mrf device becomes activated by its ID, it will accept commands from any ID numbered device/macro stream. the 2 ways to solve this are to make sure that port routing is used and that there is no cross talk within the port routing scheme...also make sure the IR blaster(s) are set to off or they will cause the problem (same for 'stray' IR signals). Solution 2 will require some trial and error but at last check the ID window is open for approximately 6 seconds so if you set the delay between system ID's to an amount greater then that you should also be able to accomplish your goals.

the follow up of this relative to your last post is that once an ID is open any code from a 'random' or 'rogue' MX remote can go out all outputs (though I have not tested this scenario)