I revisited this problem today... I was having all kinds of wierd midi issues today....
The old problem - I could assign a button on my midi control to MUTE an output. Close PROGRAM... open some other time, the remote was FORGOTTEN. I could re-assign it... but that gets annoying when it should remember it.
WORKAROUND - CREATE NEW BUS (labeled it PREVIEW). On the master bus - inserted SEND to PREVIEW bus. Routed that bus to that particular output. Assigned the button (via right clicking on the SOLO button on the PREVIEW bus) > remote control > contoller > push the 9th button on my controller > learn. WORKS LIKE A CHARM!!! :)
Now, I can save the file.... open it, and remote control assignment for that button STICKS and works like its supposed to (for me at least). Now I've got the 9th fader permanently fixed to my MASTER... and with the push of a button, I can silence everything but the headphones.