If the files already have the +x flag set, git update-index --chmod=+x
does nothing and git thinks there's nothing to commit, even though the flag isn't being saved into the repo.
You must first remove the flag, run the git command, then put the flag back:
chmod -x <file>
git update-index --chmod=+x <file>
chmod +x <file>
then git sees a change and will allow you to commit the change.