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TMS320F280049C: EPWM6A remains high for about 1 second when debugging is attempted in running code.

Part Number: TMS320F280049C

I have configured EPWM6A to generate 10 KHz duty at 50% duty cycle. When I try to debug the code while the hardware is running, the epwm is remaining high for almost 1 second and this damages the switch. I am not able to figure out the reason why this is happening. I am attaching the code as well as the DSO screenshot which shows the problem. Kindly help me resolve the issue or guide me where I am making a mistake. 

 EPWM6A_OldCompiler.zip

I have tried with 2 different versions of compiler also but I am not able to figure out the issue.