How to confuse the ECU!
The auto drop sensor in my passenger side window is a bit dicky - so today the window drops all the way to the bottom when the door is opened - oh well, it does that sometimes.
Went to raise the roof with the passenger door open (and the window all the way down on the auto-drop) - the roof came up but after locking it off the passenger window did not come up and started making a regular clicking sound.
In the end I pulled the negative lead off the battery to stop it clicking and hoping it would reset. It did and the window came up fine once the battery was reconnected.
Bloomin' italian programmers..
I think someone else was having trouble with a window clicking in the down position and not coming back up. Anyway - that seems to be the answer!