Ship Capture Issues

Try using more boarding partys if one boarding party does not work (one boarding party is not likely to work)

more partys may take over the ship faster (not sure)

ship crew can fight off boarding partys

If the attacked ship had shield regenerators, your boarding crew might have been thwarted by regenerating shields. They won't launch for a ship that still has shields, but may have launched when shields hit 0 but then the shields regenerated, and the AI got confused.

are you sure you werent set to 1/8 time? ^.^ Never heard of this. UNLESS, sometimes the crate carrying the marines just flyes in circles randomly.

maybe they got stuck in a ventalaition shaft? (It happens ^^)

besides, have you ever tried boarding a ship?? maybe it was all to much for them... (IE heart attack)

One way to run away after boarding is not putting any weapons on the boarding ship but the down side of this is that you can't board ships with shields.

Although I’ve never tried it in the simulation mode, while in actual combat I do have to control the boarding ship(s) myself. My boarding ships will typically have shield depleting weapons, and massive shielding with shield regenerators (same thing for my troop transporters, minus the shield depleting weapons). I have noticed that after the marines land, my ships still continue to fire on the boarded ships.
Before the battle starts, I pause the battle, select the boarding ships, tell each one which ship I want them to board, else they will run away, and restart the combat. Once my boarding ships drop their payload I again pause the battle, select the ship that dropped, and tell it to get the H%#$ out of there. Once the captured ship is under my control, I select it and tell it to move from the scene, or it will get pummeled. I can typically take on a fleet of up to 10 ships with this method, if I brought enough boarding ships. It takes a while to do it this way but I have way more control over the outcome. In a battle of 10 ships I will probably loose 1 to 3 boarding ships, and 3 to 5 captured ships.
I have to control my ships, including the captured ones, or I will loose everything I gained.

Theace

There are few ways I can think of: As mentioned, you can have your ship not have any weapons to begin with. Second, you can designate it to a only cause the least amount of damage (10%?) to enemies. I dont' think shields count, so that means drop shields and cause 10% of damage. You have to set it to all target vessels in the damage amount in the strategy.

Or you can set the ship to disengage when it has taken 10% of damage itself. Since the boarding parties are destroyed after launch, having enough boarding parties should trigger the disangage. Problem with this method is that if the ship is damaged before the boarding parties are launched, it will withdraw. Also if the ship has very heavy armor the boarding parties might not be enough damage to cause the withdrawal.

As fot eh boarding problem in the first place, are you running the latest version of the game(if not, which one are you running)?
Which language version is your game? (english or some other)
How long will the boarding icon stay on top of the ship being boarded? Does toxic injector work?