Hi all,
Reviving this one again, I'm in the same boat as Sharon here - as it appears many others are judging by the numerous different threads.
I would like to think that the whole point of having a Slide Master with layer/trigger functionality is that it would work when applied to a slide within your content.
I'm making a feature recommendation to add this functionality or remove it from the slide master entirely.
I've found the solution at the moment is to create a story template file, but again it is a long winded and painful process that has an end result of many unnecessary duplications of slidemater themes, resulting in unnecessarily large file sizes.