Sorry for being slow here and understand the issue now... Many ( really many) moons ago I moved all properties files into their own subdirectory, but AutoIt indeed install it into the SciTE root directory since that is also where the light version expects it.
Funny this comes up after such a loooong time, but I will have a look to fix this in the SciTE4AutoIt3 installer.
Guess all i really need to do is change this in au3.properties:
# Import the default au3.keywords.properties file containing AutoIt3 info
import properties\au3.keywords
# override with the AutoIt3 provided file located in the root.
import au3.keywords