Hello,
The FTM device allows to work in a simple mode (TPM device compatible mode) that allows "legacy" synchronization of CnV and other registers. The synchronization of the FTM device is described in the chapter 40.4.11 PWM synchronization in the K64 Sub-Family Reference Manual, Rev. 2, January 2014 or in application note AN3729 - Using FlexTimer in ACIM/PMSM Motor Control Applications.
In your case it is important to set the bit FTMEN = 0 (set the FTM mode property to Disabled) and SYNCMODE = 0.
I have verified this case in a simple demo application on the FRDM-K64F, see the attachment. You can check the signal on the connector J1, pins 1 and 3.
If you need the FTM mode enabled (FTMEN = 1) you must use the synchronization, e.g. sw trigger:
- Enable the Software triggering and CnV registers synchronization (SYNCMODE = 1 and SWWRBUF = 1 in FTM2_SYNCONF register).
- Enable Synchronization of Channels 0 and 1 (SYNCEN0 in FTM2_COMBINE).
- Select the loading point - Minimum or Maximum (set the CNTMIN or CNTMAX bit in FTM2_SYNC).
- When you write into any/all CnV register you must set the SWSYNC bit in FTM2_SYNC register (enable trigger).

I have also created a simple demo application, see the attachment.
Best Regards,
Marek Neuzil