It didn't, until I went back after totally closing everything down, so at least progress! 
Unfortunately, they still don't seem to work...
I've assigned another few Aliases to items which should be disabled (right now they should be constantly disabled, since it's a perma-run onUpdate() for testing purposes), and even though the Properties and Aliases are defined, they're not disabling...
Im running this on one of them, for example :
Alias_ZCDMSOQuest01Reference02.GetRef().Disable()
The Alias is defined, and the Property points to the right Quest Alias, which is defined as a specific Reference in the world, but that reference does not take the command. The rest of the Script works fine, and this is immediately at the top of the OnUpdate() block, so I do not see how anything lower-down would interupt it, and there's nothing else re-enabling the reference