If a D9P starts with 5" squares, the finished block size is NOT 6.5". The beginning 9 patch would equal 13.5" finished and by cutting that into quarters you lose an inch so 12.5" finished.
If you start with 4" squares, your 9 patch would be 10.5" inches and again, you lose an inch when cutting it into quarters for the D9P so it would finish at 9.5"
If you use 3 fabrics, most people put the 3rd one in the center--a dark or high contrast that will get cut very small and then your D9P will appear to have chains or steps all over.