SOLVED:
I have got my Synscan all neatly connected to my Skywatcher, placed the scope in its home position. Told Synscan to figure out where we are in the world (and it does) then I start to align.
It asks for three stars, I choose three objects (the first is Jupiter) then it goes off to hunt for him. Jupiter is in the east at the moment and the scope slews and points well below the horizon to the south. I slew all the way up the J and then tell it to go for Hadar. It slews again in an equally ridiculous direction. I slew it again this time to Hadar and tell it to go look for Arcturus.
It slews down as if to point to the earth's core when I switch off as the tube was about to collide with the pier.
Any clue as to what is going wrong?
EDIT: I had selected AZ instead of EQ in the setup of the Synscan Pro, thanks everyone.
