Please check the binary file that you are loading to verify that the bytes are at the correct locations in it.
Beware that some debuggers don't allow programming of the values in the image without first unlocking this function (for safety reasons so that people don't inadvertently lock chips).
If you secure the device I expect that after a further reset it would no longer be possible to connect with the debugger to view the registers.
I would recommend testing patterns that don't secure the flash (also in the unused 0x408..0x40b area) and reading them back directly from the flash so that you are sure they are programmed as expected before interpreting the values seen in the FTMRH registers.