Hello mariuslucianandrei,
Thank you for the response.
Yes, the synchronization of the timer and the ADC input with the flexpwm via CTU was performed, however the same issue continues to happen, which is the Resolver Sine and Resolver Cosine random data.
After that, measuring the MTRCKTSPS5744P with the oscilloscope, I could see that the timer output signal is not reaching the resolver. The measurement of "RES_REF" via Jumper J7 (connection pin 2 and pin 3) got a flat signal, instead of the proper timer output signal. Please see the picture bellow:

Just for effect of comparison, this is the measurement of the proper timer output ("RES_REF" signal) using the default Motor Control software example from NXP:

Another factor is strange. I got the correct timer output when I try my model in the MPC5744P board (Package 144-LQFP).
Is there any difference for the MBD toolbox implementation of the output timer excitation signal (Timer 0 channel 5) between the MTRCKTSPS5744P package 257-BGA and the MPC5744P package 144-LQFP?
Kind Regards, Rafael