Not sure if this is realy a bug it just seems very strange.
In a small game, I had race A getting an active scan of a race B ship.
Race A started to research communication, gets lucky and succeeds real fast.
Then Race A goes for a NAP and succeeds the first time.
Now, there are two races wich have a treaty with each other, but race B, which hasn?t have an active scan of any ship from race A, doesn?t seem to know that race A even exists. There is nothing in the diplomacy window, nor in the intel screen (well, the last one makes sense, as they haven?t scanned any race A ship, so there is simply no intel on them).
But not to be able to initiate diplomatic actions, when having allready signed a treaty seems very odd.
It's not a bug as such but rather an unintended feature

. As you say its because you haven't had an active scan of a ship which in v3.1 terms means you don't know the race exists. This is corrected in v3.2 as an alien race is recognised by an EM scan of a population as well as by active scans of its ships.
Steve