Thanks for all the replies
Wheels are ZED 45s and geometry is the same as my other bike.
Whilst it may seem that the geometry is the same; there are subtle differences, a 5mm difference in fork rake, 0.5 degrees difference in seat tube and head tube angle, 3mm difference in bottom bracket height, 0.6mm difference in stack, 7mm difference in wheel base etc.
It might not seem like much, but small changes in geometry can make a bike feel and handle different, sometimes just from how they shift the centre of gravity of you and the bike.
You could try swapping in some non aero wheels, to see how much of what you are feeling is that, and how much is the rest of the bike.