If you look at the launcher's feature tab, you will find a textfield with the complete command line used to launch FS2. Almost everything the Launcher can set in terms of options can be found here, and some of those influence the lighting.
For reference, mine looks like this: F:\Space\FreeSpace\fs2_open_3_6_10.exe -mod mediavps -spec -glow -env -mipmap -missile_lighting -normal -3dshockwave -cache_bitmaps -targetinfo -orbradar -ship_choice_3d -weapon_choice_3d -3dwarp -warp_flash -no_set_gamma -loadallweps -fps -window -output_scripting -debug_window -ambient_factor 0 -spec_exp 11 -spec_point .6 -spec_static .8 -spec_tube .4 -ogl_spec 80