I've had problems with upgrading my main website WP installation using the automatic feature for as long as I've had this host. There are several other websites that I host that are not in the main directory that I can upgrade and have never had problems. I can upgrade add-ons without issues it is just new WP releases that i've never been able to upgrade.
domain.com/ - this installation cannot upgrade
domain.com/wp1/ - this installation I can upgrade
domain.com/wp2/ - this installation I can upgrade