Troops in PBEM

[Nitram Draw]

I think there is a way to adjust the type, clasification, of ships that break formation in combat. These ships generally run to the corner for the duration of the fight.
Try removing transports from this list. It may keep them closer to the battle.
I don't know if adding a weapon will screw up the way the AI views the ship but you could try putting a capitol ship missle on them and giving it don't get hurt orders too.