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TMS320F28069M: Erratic RoverL estimation in Lab2c

Part Number: TMS320F28069M
Other Parts Discussed in Thread: BOOSTXL-DRV8301, LAUNCHXL-F28069M

I've designed a custom driver board based on BoostXL-DRV8301 and custom controller board based on LaunchXL-F28069M with the same DSP but in 80pin case. Before beginning - my custom driver board works perfectly with the launchpad. Problems begin when I attach my custom controller board. I'm trying to identify a PMSM motor. The bias values are being estimated very close to the launchpads estimation so I consider the ADCs and calculations working just fine. On the RoverL estimation step I get more noisy sound from the motor (compared to the launchpad) and when I check the PWM outputs - the output frequency is very randomised. I get perfect and stable PWM frequency when calculating the biases but on the following step the frequency becomes scrambled. I suspected my circuit wrong resulting in unstable PWM frequency but I tried  reducing it for RoverL estimation as low as 30Hz and the result was still the same. Would you advise me how to proceed debugging this?

Best,