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CC2530: Zstack interfering with regular code

Part Number: CC2530
Other Parts Discussed in Thread: Z-STACK,

I am using TI CC2530 with zigbee 3.0.1 Z-stack. I am trying to generate a 5 kHz 50% duty cycle pulse using hardware timer interrupts. Expected waveform is as shown below:

However, I see some jitter in the signal. My half wave (which should measure 100 uS) comes out between 70 uS (minimum) to 130 uS (maximum). Somewhat like as shown below:

Jitter value (60 uS) doesn't change if I change the base frequency (currently 5 kHz) or the duty cycle (currently 50%). 

However, if I comment out zigbee tasks, I get perfect waveform as expected. I feel that zigbee tasks somehow interferes with my timer interrupts due to which I am not able to keep correct track of time and hence not able to generate the exact waveform. Is there a workaround which I can implement to get rid of this problem? I need zigbee communication so can't disable it.