The pulse laser does its damage regardless. The damage is applied by the determining line in the weapon data, in the light frigate's case "DamageApplyType "BACKLOADED"" Which means it's done at the end of the Frigate's weapon 'effect'. It'll show 4 rounds fire, but a group 52.250000 damage will be applied as the last burst hits, regardless of how many rounds it fires.
For your damage change, Shmily, I think the damage was compounded because your bursts went over the weapons cooldown time, meaning that you actually got multiple 'effects' in one 60 round burst, compounding the damage into one burst.
Here's an example of the Light Frigates Weapons, with important lines highlighted.
Weapon
WeaponType "Projectile"
damageEnums
AttackType "ANTIHEAVY"
DamageAffectType "AFFECTS_SHIELDS_AND_HULL"
DamageApplyType "BACKLOADED" <--- This tells you how the damage is applied.>
DamageType "ENERGY"
WeaponClassType "LASERTECH"
DamagePerBank:FRONT 52.250000 <--- This is the damage of the weapon, per bank. This frigate has two weapon banks, which is recorded in its mesh.>
DamagePerBank:BACK 0.000000
DamagePerBank:LEFT 0.000000
DamagePerBank:RIGHT 0.000000
Range 3500.000000
PreBuffCooldownTime 5.500000 <--- This is the weapon cooldown, how long it takes to fire again.>
CanFireAtFighter FALSE
SynchronizedTargeting TRUE
PointStaggerDelay 0.300000 <--- This is the stagger between the weapon banks. One will fire, then, .3 seconds later the other will begin it's effect.>
TravelSpeed 4000.000000
Duration 0.000000
fireConstraintType "CanAlwaysFire"
WeaponEffects
weaponType "Projectile"
burstCount 4 <--- This is the number of rounds the effects show, but not the number of times it fires. Thats determined by cooldowntime above.>
burstDelay 0.250000 <--- This is the time between the effects shots... It'll show one shot, then .25 seconds later it shows the next one, up to the burst count. If you add it, it takes a full second (.25x4) to complete the four round 'effect.' With the cooldown at 5.5 seconds, the weapon has 4.5 seconds of inactivity. If you increase the burst count to 100, you have a fire the lasts 25 seconds, meaning that that 5.5 cooldown happens almost 5 times in the span to shoot one burst... So, your damage seems bigger, but the rate is the same.>
muzzleEffectName "Weapon_TechCapitalLaserLight_Muzzle"
muzzleSoundMinRespawnTime 0.400000
muzzleSounds
soundCount 3
sound "WEAPON_TECHCAPITALLASERLIGHT_MUZZLE"
sound "WEAPON_TECHCAPITALLASERLIGHT_MUZZLE_ALT1"
sound "WEAPON_TECHCAPITALLASERLIGHT_MUZZLE_ALT2"
hitEffectName "Weapon_TechCapitalLaserLight_Hit"
hitHullEffectSounds
soundCount 1
sound "WEAPONIMPACT_ENERGYLIGHT_HITHULL"
hitShieldsEffectSounds
soundCount 1
sound "WEAPONIMPACT_GENERICLIGHT_HITSHIELDS"
projectileTravelEffectName "Weapon_TechCapitalLaserLight_Travel"