As written it seems that you either put together the different regions in a wrong way or just flashed the 10 MB bios region alone. At least there in the programmer windows flashing content starts with NVRAM (first part of bios region) which is completely wrong. Use UEFIToolNE for structure and UEFITool or hex edit for changing complete regions.
FIT is part of the Intel ME tools, used for configuring ME options. It’s used for cleaning/re-initializing the ME region:
I’m away from home now for some weeks, so possibility to answer is limited.