Squish:I used FlightToolkit_1_1_31 version, taken from http://flighttoolkit.com/, the file on the one drive link you gave has FlightToolkit_1_1_32.exe , could this be causing my probs?
This is the line I pasted into command line, "C:\Program Files (x86)\Flight Tools\Flight Toolkit\ContentConverter.exe" FSX /i:"D:\Program Files (x86)\Steam\steamapps\common\FSX" /o:"C:\FlightTemp" /a
Do you have FSX installed in your PC? If so, which one, the boxed or the Steam version? You should have FSX installed in your PC so the toolkit can do its job. The line you pasted into command line is the one used when you have the Steam version of FSX. The line for the boxed version is a little bit different.