The direction and behaviour of the FlexTimer Channel signals is completely controlled by the corresponding FTMx_CnSC register settings regardless of whether the channel interrupt is enabled or not.
I think the possible cause of the issue is inappropriate configuration of a channel signal routing in the IOMUXC controller. So, please check the corresponding IOMUXC SELECT_INPUT and SW_MUX_CTL registers for selected channel signal IOMUX routing scheme. For details, please refer to the Section 8.2 "IOMUX Controller (IOMUXC)" of the i.MX7 Reference Manual document, available on the processor's Documentation web page:
https://www.nxp.com/products/processors-and-microcontrollers/arm-based-processors-and-mcus/i.mx-appl...
Have a great day,
Artur
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