I think all those C++ style comments you added are the problem, those starting with //
// is not standard for a comment in .INI file. In fact, there's NO standard for comments so, depending on the OS or the convention, some use ; others use #. Try replacing // with ; first and see if it works. If it's not, then just remove every comment, since there aren't supposed to be any in a clean prepar3d.cfg file.