Figured it out. No thanks to the search function which I think I'll take this opportunity to say is quite rubbish. I had to use google to search the form instead to find a topic similar to this one. Well this is one of those things that is not very well known and I think there should probably be something in the manual about this. Anyway the solution was to unload my script from WED and save then load it again and restart WED. It does not work if you do this
include = <myscript.wdl> //DONT USE = SIGN

such a bizarre thing.