It may also have something to do with how colors are paired up? So far, I've always done the "draw the diagonal, stitch 1/4" from the line, and then cut them apart" method. It has worked out okay so far. I'm afraid I'm not a gentle enough soul to work with the diagonals already cut.
Cathysews posted this awhile back:
I saw this on one of my other groups and I Love it. You layer 2 squares facing. Sew 1/4 inch around all four sides then cut each way from corner to corner cutting into 4 pieces. When you press them open - all seams to the darker side, you just lay them out ready to sew together. All pieces are the same size. The same lady posted a chart of sizes for different squares. Remember that these measurements are for the 4 square you get - NOT the finished pinwheel.
2" squares = 1" HST
2 1/2" = 1 1/2
3 1/2 " = 2"
4" - 2 1/2
5" = 3 1/2
6" = 4
7" = 4 1/2
8" = 5"
8 1/2 = 5 1/2
9" - 6
10" - 7