Hello,
I have found my mistake.
The reference manual has this note:
"If MCTRL[LDOK] is not set, setting MCTRL[RUN] also sets the STS[RF] flag. To prevent a CPU interrupt request, clear INTEN[RIE] before setting MCTRL[RUN]."
I am using STS[RF] to end PWM cycle, but I clear STS[RF] before doing MCTRL[RUN] = 1.
Thanks