After successfully machining the first flat, it tried to machine the second flat about 10mm above the stock - WTF?? Obviously it didn't succeed on that operation so I stopped it.
Modified the position of the WCS (moved from top surface of stock to centre of circular end face) and reposted. This time it went as intended. Still not sure what the issue was, as I double checked for silly mistakes and it's not obvious (or too obvious??).
Here we go finally:
Worked out well.
Now to attempt a wrapped toolpath. Note that 4th axis operations are limited to 2D toolpaths (2D Adaptive, 2D Pocket and 2D Profile). For true 3D surfaces I'm guessing you need to check out true multi-axis (ie 5 axis) operations. One step at a time....