From: St. Petersburg, Florida, USA
I've been playing this game and its ancestors (WitP and UV) for 17 years. I've never read the manual. (Some of you will now interject, "Well, that explains some things....")
If you come equipped with a love for and knowledge of the Pacific War, the game is amazingly intuitive. You know that the Japanese are the aggressors early, that losing carriers is a bad thing, that sinking enemy carriers is a good thing, and that Hawaii is more important than Samoa. So you begin small, playing Guadalcanal or some-such against another newbie or a patient veteran and you start to learn. You make a zillion mistakes. You read the forum and pick up tips from the incredible Peanut Gallery that inhabits these parts. And you find that it's worth it because you plan to be engaged in the game for years - indefinitely! - forever! So it doesn't matter if the learning curve is steep. In fact, that's an attribute, because that means the game isn't likely to grow stale.
And you're careful about disagreeing with veteran players, because you know they typically know what they're talking about. Like Anachro. He knows what he's talking about. He's played a long time. He reads. He contributes. He's built up a large reservoir of good will.
And he's right - you never put subs on computer control. You mostly set them to patrol. When they run low on fuel or ammo, or incure moderate damage, they'll retire to port to replenish/repair. If repairs aren't necessary, they'll return to their patrolling station, just exactly as you wanted. And just like Anachro said they would.
The problem you have is that you probably didn't set your subs to "Patrol." You probably used "Remain on Station." Because the "Patrol" functions works perfectly and contrary to what you're describing.
I set them to patrol. They seem to patrol once when on human control.
How did you send them to 'patrol'?
Patrolling is a distinct set of orders and has a defined meaning in game terms.
Patrolling is a form of computer control accessed in a very different way than the Player Control/Computer Control/Continuous Supply clickable yellow text.
I'm not at home and in front of the game where I could grab screen shots to better explain.
The patrolling interface is accessed on the second page of the TF interface, a page you may not know exists.
To the right of the TF picture there are several lines of yellow (clickable) text one of which will take you to teh second page of the TF interface. There you can set waypoints, give orders to follow, meet etc., establish threat tolerances AND establish Patrol patterns, either by letting the tactical AI lay out a pattern or by individually assigning up to three hexes to establish a patrol pattern. You can control number of days on station at each hex and if refueling will be allowed and to what degree (in case you establish one of the hexes in a port).