Have you scoped your arduino output to verify you are sending proper signals to the scanner amps? That would be my guess. It looks like the pulses are somewhat periodic in X time. Almost as if you have a square wave riding on your Y output. Since scanners are analog devices, that strongly suggests that the problem is not with them. So, my guess is something funky is going on with your arduino output. How are you converting the arduino output to analog voltages? Hopefully, not PWM.