So like many others have pointed out the part cooling fan starts automaticly on the first layer even though the fan speed is set to 0 for the first 4 or what ever layers if the "Increase fan speed for layers below" is enabled.
To avoid this, and the input of other random unwanted "junk" gcodes getting fed in before our custom start scripts couldn't it just be an Disable/enable automatic start script generation button inside the Scripts->Starting Script tab?