Comment 10 for bug 1302770

You could probably set it in xorg.conf.d, but I wish there was a better solution. This problem keeps coming up, infrequently, but persistently over the years.

OK, let's see. The indicator in unity panel writes to gsettings.
gsettings monitor org.gnome.desktop.input-sources current

Unity-settings-daemon listens for this key's changes and in response sets the root window property _XKB_RULES_NAMES. As I understand it, that's basically what setxkbmap does too.
xprop -root | grep XKB

However, unity-settings-daemon seems to always add the us layout as a second group, something "setxkbmap it,us" would do.
setxkbmap -query | grep layout
layout: it,us

I don't know why that happens. There's probably a good reason for it, but I could imagine this is what exposes you to the old bug #837456.