I've only done one pinwheel quilt but I found if I put my blocks togethr left 1/2 to right 1/2 instead of top 1/2 and bottom 1/2 they lined up much better. Don't understand why but that's how it worked for me.
I'm usually not a pinner but found that I had to with pinwheels. I pinned each seam, both sides where they met, and then just a hair to the left of the seam.
Hope this helps.