@Bio_TICFSL . I am using the BSP provided by Toradex for WINCE 7. Also wanted to highlight that the registers for FTM in the refernce manual are in big endian, while the registers for the other hardware are in little endian. Please have a look, I think FTM registers should be in little endian format as well.
I've just had a conversation with Technical Support about that. Proper bit configuration in registers is described in Vybrid VF610 reference. In IMX7 docs bits are reversed not only for FlexTimer but for Ethernet modules too.