The T-1 is presumably supposed to be what causes the system to return any existing tool before picking up the new one??
However you are spot on correct, the toolchange system works perfectly if that line is removed / commented out!
It was in the E3D toolchanger template files I found, and it worked fine with those files, just changed tool positions, when I first set up the Duet on V3.3, so I have no idea at all why it messes things up now? That was the really confusing thing.
Oh well, I can start recalibrating everything now and hopefully get it printing.
Thanks!