A big thanks to Justin (Doubledip)...
I spoke to Justin on the phone and he asked if I had an Auto program in it. I started to doubt myself as to whether I had actually flashed in the wrong program.
I checked the program and it was definitely an Auto tune. So I was initially a bit bummed out, having thought it could have been an easy fix.
I then thought I would just try flashing in a stock Auto tune, (just a stock VY Berlina tune). Well what do you know, as soon as I fired up the scanner I could see the PRNDL status was in neutral (it had always been stuck in Park). Then as I flicked through the gears the PRNDL status changed each time.
I haven't actually fired up the car to see if it's fixed, (as it was late last night and my neighbours would not appreciate the noise), but I am 99% sure that it was the problem.
Thanks again Justin.