Many people have had trouble with getting the Return to Base directive to work right. The problem usually manifests in the directive showing up far too early, sometimes even at the very start of a mission. Below I will go over the most common reason why this happens, and how to avoid it.
The directive appearing at the start of the mission is caused by the way directives work. A directive will be displayed not when the event it is tied to becomes true, but when it is logically possible for the event to become true. The mistake many new FREDders make here is making an event that becomes true when the player jumps out, then attaching the RTB directive to that. It shows up immediately, as the player can hit Alt-J any time he wants and as such it is logically possible for the event to become true right from the start of the mission.
It is also possible to have it pop up mid-mission. This tends to be in escort missions where the mission designer has the RTB directive dependant on both the escorted ship and the player jumping out safely. In this case, it shows up not at the start of the mission, but when ship to escort arrives in the mission, since as soon as the ship is in the mission, we once again have the situation from before where it is logically possible for the event to become true - Both the ship and the player are there, so both can jump out any time and fulfill the requirement.
The solution to both these situations is event chaining. A chained event cannot under any circumstances become true until the event is is chained to has become true. So, have the RTB directive on a separate event, chained to another event that completes when the mission is complete. Then the RTB directive will not show up until the player is actually supposed to jump out.