With MM and Kingroot, that is what happens. If you reboot your phone, you have to run Kingroot again to root it. It will stay rooted as long as you do not reboot.
And there isn't any other rooting method for the MM version. I myself don't use Kingroot. It's from China and it uses the internet to supposedly download the latest version, but who knows what else it does? In fact, I'm not even rooted. No reason to be rooted for me. I used to root due to Titanium Backup, but the LG G3 comes with a very capable backup utility built into it in the settings section that does the same thing TiBu does as far as saving and restoring app settings.