I don't run any conventional engines or have a need to vary the track voltage with the Cab2 remote. I just set my fixed voltages with the handles and bring up the layout with an on/off switch.
Why do you need command mode for the Track power?
Anyway, do the outputs equal one another in non-command mode? Are the outputs equal at the A,B,C.D and U terminals without the meters connected? The meters do have a small resistance. Disconnect them as a potential load causing the variance,
This is an issue that you have to isolate by working your way from the start. Bricks are good and equal-check. next...
The slow switch may just need some mechanical tuning. Check the lantern bar for drag. Also, if you changed sides, there is a run that didn't have enough clearance for the lantern bar where is passes through the roadbed. Also, the motor screws may be too tight. Loosen the an 1/8 to a 1/4 turn to take motor pinion gear pressure off the segment gear.