Once they've run out of things to do, they do tend to just stop. The AI tends to use Flagships purely for anomalies - once they've gone, it parks it there forever. They use scouts to explore.... it would be a good idea if the AI could switch from using the flagship survey routine to the explore one. You will also notice that when scouts find something they're interested in, they tend to stay there for a while - this isn't such a problem as it gives them a view of whats occurring there.