I am going to try a simple copy and paste from my 1946 config into the CoD config and see if the values are recognized at all. These entries in CoD will be placed under the same spot as the 1946 ones(rts_joystick).

The only thing under this in the CoD config is FF=0.
I copied and pasted this from 1946:

[rts_joystick]
X=0 1 4 9 16 25 36 49 64 81 100 0
Y=0 1 4 9 16 25 36 49 64 81 100 0
Z=0 10 20 30 40 50 60 70 80 90 100
RZ=0 10 20 30 40 50 60 70 80 90 100 0
FF=0
U=0 10 20 30 40 50 60 70 80 90 100 0
V=0 10 20 30 40 50 60 70 80 90 100 0

I will test this now and report my results here.