Thanks for you help guys, we have a winner!
My new tough metal core belt turns out to be not so tough and must have softened (probably from friction/heat) at some point and has actually stretched in the area over the toothed pulley.
I checked the movement as @T3P3Tony suggested and it was elongated near the centre of the bed's Y axis but not towards the edges. After @hurzhurz mentioned his issue with his Anet belts I then went and checked the belt and found this:
You can actually see where the rubber has stretched and increased distance between the belt's teeth!
Thanks again for everyone's help - turned out to not be a duet related issue at all but you guys got me looking in the right place.