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TMS320F28069M: Wrong ADC measurement while using PWM under CLA task

Part Number: TMS320F28069M


I am using TMS320F28069M processor for a project using Simulink as software platform. I am operating three PWM using CLA Task hardware interrupt function by keeping CLA Task trigger inside ADC Task hardware interrupt function. The CLA task trigger function is generating three phase reference signal for PWM which are written in three memory block. I used CLA1toCPUMsgRAM option while declaring the memory. The PWM is generating output using the voltage reference from these memory from CLA interrupt task of main processor. The oscilloscope measurement of output voltage is correct. But the internal ADC measurement of three phase output voltage is not correct. I have checked it using SPI communication. Somehow the ADC and PWM are not synchronized in the program. 
Observation: The PWM is not generating any output signal If I checked the checkbox of ADC continuous mode after the post interrupt of end of conversion (EOC) as shown in the example. 
I appreciate any advice in this regards. Thank you!
I am following an MATLAB example (Task 4: Permanent Magnet Synchronous Motor Field-Oriented Control (FOC) Using CLA) from the link (www.mathworks.com/.../using-the-control-law-accelerator-cla.html).