Unless you encountered some kind of bug, the only reason your nations wouldn't be able to spot one another is if they don't have tracking stations. Normally when you create a new race, they automatically have one at their homeworld. Now I know you said 'space scanners' but I'm not sure what you meant by that. If it's some kind of base with active sensors, it won't work - you can only detect a colony by passive sensors, which most of the time means tracking stations.