From the comments in pwm_tones.c in SDK 2.2.0, pwm_transitionToSubstituteValues() is NOT glitch free while pwm_startWithAlternateValues() is glitch free.
Can you make a double check?
Yes, you are right, pwm_startWithAlternateValues() is glitch free because it first disables the channel, reinitializes the PWM configuration and then enables it. On the other hand, pwm_transitionToSubstituteValues() reconfigures the PWM HW while it is running, so there might be some glitches/incorrect PWM frequency for one cycle.
Understood. thanks a lot:-)