PWM output jitter

Hello all, 

I am trying to use TMDSDOCK28035, piccolo experimenter's kit to run a three phase AC motor. Following is the code where I set the PWM outputs, 

//set compare registers
EPwm1Regs.CMPA.half.CMPA = compValue[0]; //PWM 1A - PhaseA
EPwm1Regs.CMPB = compValue[1]; //PWM 1B - PhaseB
EPwm2Regs.CMPA.half.CMPA = compValue[2]; //PWM 2A - PhaseC
EPwm2Regs.CMPB = 0;

and these are sent to the GPIO pins using the following code 

GpioCtrlRegs.GPAMUX1.bit.GPIO0 = 1;                     // 0=GPIO,  1=EPWM1A,  2=Resv,  3=Resv

GpioCtrlRegs.GPAMUX1.bit.GPIO1 = 1;                   // 0=GPIO,  1=EPWM1B,  2=Resv,  3=COMP1OUT

GpioCtrlRegs.GPAMUX1.bit.GPIO2 = 1;                     // 0=GPIO,  1=EPWM2A,  2=Resv,  3=Resv

When I look at these pins on the scope, I see the PWM outputs but they have jitter, the edges seem to vary around 20us and PWM interrupt is running at a rate of 10khz. Because of this my mosfet gate drive outputs also has the same jitter. How can I avoid this?

Appreciate any inputs.