Right, I pulled my FSC with e-sys, base64 encoded it using
http://www.motobit.com/util/base64-decoder-encoder.asp
Copy paste into a new file on a SINGLE LINE and save as FXXXXXX_0001B001.fsc for CIC or FXXXXXX_000DE001.fsc for NBT where FXXXXXX is your VIN.
Then downloaded BMW_CIC_NBT_FSC_Generator.rar from
https://mega.co.nz/#F!ugo0HB5L!TPCmejMKPBlRRkz2SDvg0Q
Followed those instructions:
Generating FSC code for CIC systems, copy fsc.exe in the "CIC_FSC" to "tools"
Generating FSC code for NBT systems, copy fsc.exe in the "NBT_FSC" to "tools"
Drag and dropped my base64 encoded FSC into the GUI and selected the correct map, clicked GENERATE.
It didnt work the first time, I didnt put the correct VIN in the file name, this seems important since I changed it to the correct VIN, tried it again and my NAV accepted the code without problems.