[Suicide Junkie]

Is it possible that an enemy ship appeared and caused the colony ship to stop? And were the ship's orders cleared?

It could be a difference between simultaneous and sequential.
Perhaps modding a solar supply generation of 1 point into the colony module would help.
Then colony ships would always have two MP when they're "out" of supplies, and always have 1 supply at the beginning of a turn to land with.