Half Sidecar PWM Ports Working

[Toa Circuit]

Check to see if they really are getting a forward or reverse signal. Green on the Jags is forward, red is reverse.

Why do I ask? I'm guessing you're using ports 1, 2, 3 and 4 for your drive motors. 3 and 4 are on one side, correct? If so, then everything is working as it "should", just not what you are expecting. (Since on a normal FRC drivetrain, the left side is a mirror image of the right side, and the motors are rotated 180 degrees...) You'll need to change your code to drive motors 3 and 4 inverted, or on the OUTPUT side of the corresponding Jags (The side with M+ and M-), make the motor's red go to M- and the motor's black go to M+.
If that isn't what you're doing... then something very strange is going on indeed.

EDIT: I guess I didn't understand your problem correctly. You're saying that the problem isn't inversion but lack of control?