I have a 7900 that I have recently converted to Piezography and it took three INIT FILLs with PiezoFlush to finally get all the color out of my test prints. After the first INIT FILL you should see PF printing from the Nozzles but probably with a lot of color tinting from the color ink stains still in the system.
In my experience, it is normal for some of the ink tubes to look like they still have color ink in them after the first INIT FILL, especially the Cyan, Photo Black and Matte Black lines. The Yellow line may also still appear yellow. The tubes actually have PF in them after the INIT FILL, but the color ink leaves strong stains on the walls of the tubes and it makes it look like the color ink is still there.
After the 2nd INIT FILL, you should see the tubes start to look pink, and by the 3rd INIT FILL I believe you will see all pink. So my recommendation is to do at least one more INIT FILL, and maybe two. Just be sure you have enough PF in the carts and keep track of your maintenance tank. In my 7900, the PF level in each cart went down about 1/2 inch for each INIT FILL; for your 9900 it would probably go down even more since your tubes are longer.