Hi Filippo,
I might have ran into the same issue.
I created a relationship between users and a custom posttype today and same thing, after selecting a user and updating the post, the edit post page reloads, but the selected user is not showing.
I examined the database, the data is getting saved, but somehow the code is not picking up the saved value, so the next time around the metabox is unselected again.
Hope someone from the Metabox team is able to investigate this issue
Thanks,
Ruud