Yes, your analysis is quite right. There seems to be a period of time, a lag, between the moment of spawning and the moment you can affect an NPC. Possibly you could just wait a while in a script before trying to affect, although I can't verify that, since it wouldn't really have suited my purposes. I have solved the issue by prespawning NPCs shortly before the cinematic, not in the cinematic script itself.
Also you should notice that spawnscripts do get executed always, but that of course disperses the cinematic script, and with the signalling approach, that's not something to be desired.
So, my advice is to spawn pretty much all the npcs you need in a cinematic just before you launch the actual cinematic script, not in the cinematic script itself. Well, there might be other ways, but this is the one I chose.
Run command does work, but it's sometimes a bit tricky, and may seem a bit less reliable than a script_runner. Make sure you have the path right and everything. But this won't necessarily solve the problem of affecting newborn npcs, mind you.
Frozen by ICARUS