Hello,
I am not sure if this can be problem - at least it is proably not correct:
when adding a key to an empty section and deleting the key so that the section is empty again, every add adds the section-name again - example:
git config gc.autoDetach false ; git config --unset gc.autoDetach ; cat config [gc]
git config gc.autoDetach false ; git config --unset gc.autoDetach ; cat config [gc] [gc]
git config gc.autoDetach false ; git config --unset gc.autoDetach ; cat config [gc] [gc] [gc]
Git-version is 2.17.0 Linux - Cent/OS: 2.6.32-754.10.1.el6.x86_64 - GNU/Linux
Greetings Kurt