Okay, sounds like you have it figured out and could enlighten the rest of us with your filament settings. I'll illustrate the issue.
As shown in the following two images of the same simple cylinder that was intended to gradient by 10% from green to black. Each step change in mix ratio was to occur every 10 layers. I stopped the print once I saw it had mixing problems. As shown, when two filaments are simultaneous feed into the nozzle they come out not homogenized but merely adhered to one another (as in the lower diagram). This results in seeing the green at certain locations of the part and black at other locations (red circles). Clearly this is a result of how the nozzle is positioned and traveling. If they were truly mixing to some level of homogeneity than this directionality wouldn't occur.