Tom
Below is code showing how to set up a PWM signal on the output that you are interested in.
This is API code:
PWM_INTERRUPT_SETUP pwm_setup;
pwm_setup.int_type = PWM_INTERRUPT;
pwm_setup.pwm_mode = (PWM_SYS_CLK | PWM_PRESCALER_16); // clock PWM timer from the system clock with /16 pre-scaler
pwm_setup.pwm_reference = (_TIMER_0 | 3); // timer module 0, channel 3
pwm_setup.pwm_frequency = PWM_TIMER_US_DELAY(TIMER_FREQUENCY_VALUE(1000), 16);// generate 1000Hz on PWM output
pwm_setup.pwm_value = _PWM_PERCENT(20, pwm_setup.pwm_frequency); // 20% PWM (high/low)
fnConfigureInterrupt((void *)&pwm_setup); // enter configuration for PWM test
and this is the low level code that performs the actual work (I have also noted the HEX values that are actually written to the FTM registers)
POWER_UP(6, SIM_SCGC6_FTM0); // ensure that the FlexTimer module is powered up
_CONFIG_PERIPHERAL(A, 6, (PA_6_FTM0_CH3 | PORT_SRE_FAST | PORT_DSE_HIGH)); // FTM0_CH3 on PA.6 (alt. function 3)
ptrFlexTimer->FTM_channel[ucChannel].FTM_CSC = FTM_CSC_MS_ELS_PWM_HIGH_TRUE_PULSES; // FTM0_C3SC = 0x28
ptrFlexTimer->FTM_CNTIN = 0;
ptrFlexTimer->FTM_MOD = (ptrPWM_settings->pwm_frequency - 1); // set the PWM period - valid for all channels [0xc34]
ptrFlexTimer->FTM_channel[ucChannel].FTM_CV = ptrPWM_settings->pwm_value; // set the duty cycle for the particular channel [0x271]
ptrFlexTimer->FTM_SC = (ptrPWM_settings->pwm_mode & PWM_MODE_SETTINGS_MASK); // note that the mode is shared by all channels in the flex timer [0x0c]
Finally here is screen shot of the FTM registers after the configuration so that you can compare with yours and seen if there is something missing or different:

Regards
Mark
Kinetis: µTasker Kinetis support
K60: µTasker Kinetis TWR-K60N512 support / µTasker Kinetis TWR-K60D100M support / µTasker Kinetis TWR-K60F120M support
PWM: http://www.utasker.com/docs/uTasker/uTaskerHWTimers.PDF
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