From: My Own Private Hell
I have no issues with keeping manual control.
I, on the other hand, have many issues keeping manual control. I have a save that I can supply where it's Impossible to keep a fleet on a designated spot (at least I can't), irrespective of the posture/stance, range I choose. After a while, probably because they're attacked by enemies, some elements of the fleet leave the rendezvous point and decide to assault the enemy space port on the other side of the system. I tried defend/minimal range/only when attacked and other passive combinations to no effect.
Probably a silly question but have you looked in the options screen? Click Empire Settings, the default AI stances for ships are in there, never tried them myself as I do not have the problem but there is one for other that might be the one you are looking for.
Here is how I control fleets for engagement.
In the options screen click Empire Settings change the refuel and regroup settings both to 90. I do this for every game so once set you can forget about it.
Lets say I have two fleets, Attack 01 (attack ships) and Invade 01 (transport ships).
Attack 01 is on the 1 key and Invade 01 is on the 0 key
I now select the enemy system that I wish to conquer by zooming out just to the point that I can click on the system and it becomes highlighted with a circle around it. Now click on the info box to center the view, next I send Attack 01, press 1 and right click just outside that system circle, Attack 01 should now have a 'Move to ...' command. Now do the same for Invade 01. Both fleets are now 'parked' outside the system you wish to attack and will not move (the fuel setting in the options screen helps with this as well)
Now that I have my fleets parked I select the system again that they are parked out side and check the info box for the planet, click on the planet to center it and press the home key to go direct to the planet. If you have researched Proximity sensors you should be able to see any defenses the planet may have, press 1 for Attack 01 and right hand on the planet or any base, defensive base and select 'Prepare and Attack ...'Attack 01 will now move to attack that target while Invade 01 waits, once the once the planet is 90% cleared of defenses I press 0 for Invade 01 and right click the planet, press 1 again to select Attack 01, just to make sure the way is clear for the troops.
Rinse and repeat for the rest of the galaxy. Once you get used to doing it this way you can gauge how close you can park your fleets before they start to move to intercept other enemies in a system and also how long to leave it before calling in the transport fleet for invasion, one other thing to note is once the invasion is underway issue an order for your transport fleet to orbit the planet you are attacking and check there engagement order is 'engage when attacked' that does a fairly reasonable job of keeping them out of trouble.
The best thing about this method of control with fleets is that you can order multiple fleets to sit outside systems, I quite often in mid game invade 8-10 systems at the same time, the fact that the fleets can be parked up just outside a system means that you can send them and not worry about them moving, while your fleets are moving into position you can do other things, then once war is underway you can hit the enemy at multiple fronts and it loses systems on multiple fronts all at the same time, as the war weariness is always adding up this way ensures a clean decisive victory in the shortest possible time.