Greyed out end patrol would mean you are not at your "currently assigned" home port or you have not fulfilled your primary assigned mission. Maybe you expended your torpedoes on non-mission objectives. You should get your torpedoes replenished at non-base refits though. If not, this might indicate your game is broken or a mod is causing problems. Remove mods, and/or reinstall game directly applying latest patch and make sure you use the CD to play the game.
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