Ok, so I changed the baud rate and when I hit "Scan" it found my engine and gave all the details, however when I tried to connect it said I had to check the ELM>ECU settings. So that didn't work for me.
I did have some success though, I took the face off the new window switch unit and put it on the old one and it's gone back to normal. So I now have working windows and no flashing odometer.
Thanks everyone for the advice. Hopefully if anyone else has the same problems as me then they will know that this method is a really easy fix.