@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.
Usually in Big Endian notation, for 32-bit word, bit 0 is the Most Significant Bit (MSB),
and bit 31 is the Least Significant Bit (LSB).
In Little Endian notation, for 32-bit word, bit 0 is the LSB, and bit 31 is the MSB.
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.