Hi ozgun,
please, could you send the screenshot with the parameters?
It looks that Rs and Ld, Lq are measured wrongly. The engine should have very low time constant (L/R). Method that MCAT calculates parameters of regulator would return negative values if you would select lower value than 1041 (this is the reason of the message).
If does your engine have low time constant, you should select higher values with PWM (the same for frequency calculating FOC), for example from 10kHz -> 20kHz).
Also depends, what KV family do you use. For KV10 is 20kHz is too high.
From your second print screen is not see that the update does not work.
Best Regards,
Iva