LUA needs to be ran server side and not by the player. For as long a construct is spawned or the core is intact LUA scripts should be linked to the ship and not the player when the Prog Board is activated, and would run indefinitely so long as the core, Board, section the board is mounted on, power systems (when they eventually get added), and spawned state remains intact or not completely destroyed.
At the very least, it should autolink to the nearest player who has rights that enters the ship if it isn't already linked to a player (providing the board is activated). Also, link range should be just as far as container linking, or at least a skill.