I do think it is the type of class the ship is. I've changed the gunboats class to 3 I do believe and the fighters only attack the gunboats but run from the battleships. I am not really familar with getting NPC to attack BS's but that's what I did.

Well, i'd say its due to the behavior of the encounter's ships. Try someting along these lines.. This is from pilot_pop:
[JobBlock
nickname = assault_job
wait_for_leader_target = True
maximum_leader_target_distance = 2500
flee_when_leader_flees_style = True
scene_toughness_threshold = hard
flee_scene_threat_style = hardest
flee_when_hull_damaged_percent = 0.200000
flee_no_weapons_style = True
loot_flee_threshold = hardest
attack_subtarget_order = anything
field_targeting = always
loot_preference = lt_potions
combat_drift_distance = 25000
attack_preference = fighter, 5000, guns / guided / unguided
attack_preference = freighter, 5000, guns / guided / unguided
attack_preference = transport, 5000, guns / guided / unguided
attack_preference = gunboat, 5000, guns / guided / unguided
attack_preference = cruiser, 5000, guns / guided / unguided
attack_preference = capital, 5000, guns / guided / unguided
attack_preference = weapons_platform, 5000, guns / guided / unguided
attack_preference = solar, 5000, guns / guided / unguided
attack_preference = anything, 5000, guns / guided / unguided

instead, create:
[JobBlock
nickname = bomber_job
wait_for_leader_target = True
maximum_leader_target_distance = 2500
flee_when_leader_flees_style = True
scene_toughness_threshold = hard
flee_scene_threat_style = hardest
flee_when_hull_damaged_percent = 0.200000
flee_no_weapons_style = True
loot_flee_threshold = hardest
attack_subtarget_order = anything
field_targeting = always
loot_preference = lt_potions
combat_drift_distance = 25000
attack_preference = capital, 5000, guns / guided / unguided
attack_preference = cruiser, 5000, guns / guided / unguided
attack_preference = gunboat, 5000, guns / guided / unguided
attack_preference = weapons_platform, 5000, guns / guided / unguided
attack_preference = solar, 5000, guns / guided / unguided
attack_preference = fighter, 5000, guns / guided / unguided
attack_preference = freighter, 5000, guns / guided / unguided
attack_preference = transport, 5000, guns / guided / unguided
attack_preference = anything, 5000, guns / guided / unguided

Then add a new encounter, called area_bomber if you want to add a specific fighters vs capitals at set areas. Or you could just change the capital ship encounter to be similar to:
[EncounterFormation
ship_by_class = 1, 1, sc_battleships
pilot_job = bomber_job;<-----
make_class = wanderer
ship_by_class = 2, 2, sc_cruisers
pilot_job = bomber_job;<-----
make_class = wanderer
ship_by_class = 1, 2, sc_gunboats
pilot_job = bomber_job;<-----
make_class = wanderer
ship_by_class = 1, 1, sc_fighters
pilot_job = escort_leader_job
ship_by_class = 1, 1, sc_fighters
pilot_job = escort_job
ship_by_class = 1, 2, sc_fighters, -1
pilot_job = escort_job
formation_by_class = battleships
behavior = wander
arrival = All
allow_simultaneous_creation = no
zone_creation_distance = 1000
times_to_create = infinite
[Creation
permutation = 0, 3
That will make the ships attack each other more. The best way of getting fighters to attack capitals is to add a ship class and give them unique loadouts armed with torpedos and higher level mines. But, its up to u.

I herd if you give them all ship class they will kill eachouther like normal where I change that?

-------------------------------------
"You dont see me, you dont hear me, but you know im there."
I will bild the first Galactic Empire!

Err, sorry which ship_class did you want? The fighter one?

It's all in the shiparch.ini loud and clear..

Ok I =found it and yes I wnat it to be fighter cuz fighters attack eachouther and enything.

-------------------------------------
"You dont see me, you dont hear me, but you know im there."
I will bild the first Galactic Empire!