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TMS320F2800137: PWM changes frequency by itself

Part Number: TMS320F2800137


Tool/software:

We have a basic program that we have been using and testing for a few months. Basically a pwm set up at 20khz, gives an adc interrupt at which some adcs are read. All our functionality happens in a single ISR which ofcourse needs to finish its computation in 50 us. We have changed number of ADCs /PWMS and added a lot of different tests and control functions, everything was working perfectly until a few days ago we noticed our pwm frequency decreases at odd changes in code . 

The code only passes value of cmpa to the pwm bloack to change the duty cycle. We donot change the TBPRD value for the epwm at any point , it stays as configured initially . But our pwm frequency changes .

Any clue what could be causing this ? This is appearing in our previously tested codes as well. It could be a hardware error, but it occassionally works fine as well. Any insight would be useful .