When I switch to twenty Twelve, my menu doesn’t appear at all.
My theme is Timeliner. The menu seems to be managed by WP as usual.
I’m gonna ask them about how it works.
Your plugin works fine the only thing is the “alt”, not the flags but on the name of the language (since the last version it has changed)
As you can see here when mouseover “English” : https://i.imgur.com/lSwedtL.png