I bumped on this very same problem about layer visibility just 2 days ago and I can say that I'm also disappointed that this doesn't even mentioned in the manual.
I spend whole yesterday trying to figure out what was I doing wrong. Tried with different settings, different methods, I read manuals about layers, system action/expression, etc. all with same result. Jeez, it even cross my mind to rewrite everything because I wasn't sure if the bug was coming from corrupted save file. That would have set me back a week worth of works. This should have been mentioned in the manual.