Downloaded and started B3, started a new game, and set the original two ships in motion, first the survey ship with the "A" command (autosurvey) and then the colony ship by right clicking a destination some 10 tiles away. The survey ship moves automatically and explores anomalies successfully, but the colony ship just sits there (it was three or four turns before I noticed it hadn't moved).
Once I discovered that the colony ship was not moving, I moved it manually for a couple of turns then set it to a new destination and now it is moving.