Help with encoder

I have Gecko 340's. I have 500 line rotary encoders on my servos.
The color code of the encoder wires is Red, Black, Yel, Wht, Org, Blu
and Brn. I put the motor on the bench and with a scope determined
that (as expected) red is +5, blk is Gnd and that I had out of phase
signals on the yel-blu set. The wht-org set are from what I can tell
the differential outputs of the A and B (?) The other wire are INdex
and signal grounds.

Here is my problem. The machine runs but the math doesn't seem to
work (almost like I am getting 1000 pps in quad rather than the 2000
I would expect.) I am concerned that I have picked a differential
pair as the AB set. Is there a standard color code? How could I
setup with a dual trace scope to determine which leads are the REAL A
& B signals. The 340 uses single ended inputs. How could I tell if
the primary pair is supposed to be yel-wht or blu-org?

Something wierd is going on.

Here is the math that doesn't seem to work out:

Leadscrews 5 TPI; pulleys 4:1 ratio; encoders 500ppr; Gecko set to
divide by 5.

By my calculation that should be 20 * 2000 / 5 for pulses, or 8000
per inch. That setting drives the table almost 2X that distance.
Halving the steps gets it closer. I have not had time to setup a
dial indicator but it appears to be gaining steps because a return to
0 command moves it back past the original 0 points.

Like I said: something weird is happening....help