Thanks Dave. I've managed to crack it and will attempt to explain - hope it makes sense?
There are some Prolific drivers required for the Serial port. These need to be installed and the ports aligned in both device manager and the software. Baud rates have to be syncronised as well. This doesn't explain (to me) why the usb ports work after serial port drivers are installed but I'm not complaining - it's working and I can now program the scanner from the lappy which is much, much easier
Al
Edit: Sorry, it's the Uniden 3500XLT