Second test:
Bug: I commented and cleaned my config file to include"commented headers" etc.
When I started the sc_trans it wrote a new config file removing all my comments and including all my "commented" i.e ";" started lines in the new file as actual lines.
So the re-write config file option is bugged.
EDIT:
It put all the options in alphabetical order removing all comments...
Now everything is removed from their corresponding comment sections.
Bugged