I think the problem is that you're inputting 360 in the angle for the polar array, and it's causing an overlap of the last instance, and that's giving it fits. Just manually draw out the radial extent to be something like 45 degrees to create the array, then manually drag the extents to 360 degrees, and it works fine. Then you can click on the temporary dimensions of the array to set the radius (no need for a cirucular reference line as I suggested earlier, sorry), and assign a parameter for the quantity. Seems to work OK then.
My main problem was that the array would work on the family but when I tried to 'flex' it to a different size Revit would refuse to change the array. Simple fix was to ignore the dimensions A and B (see earleir posts) and just use the pitch circle diameter that the bolt holes were on. Also, ignore rotating the array in the family that hosted the array.
I used three families in the end - the host being the one that held the rotation angle (I still had to use a group in order to rotate the array without errors occuring when flexing the various sizes).
As an added bonus I added a shared parameter instance angle - meaning that when the flange is in a project and requires an 'odd' angle I can simply change the shared angle parameter.
All working well so far but I will continue to do more testing.