Script not working

I played over 100 turns as Pergamon and the script always came on. Then I played as Boii and Aedui and the script came on once but never again (during the first session but after closing not again). I'm used to the advisor telling me to activate the script every time I load a game but this isn't the case for these two factions. Is there something wrong or is this normal?

Eh, I think you just weren't reading what advisor actually says. In M2TW engine, campaign script is always loaded when starting or loading a game, so there's no triggering via advisor as it was in EB I. However, when playing as hellenistic faction, Romans and probably some more, advisor often pops up to remind you that you have colonsits free to settle (meaning you can build a "colony" type building in one of your cities). That's probably what you're confusing with campaign script.