I notice that when I use the ECM shield, it doesn’t do squat to protect me against EMPs. When I tried to make my own module with increased effectiveness, it doesn’t work, every single shot still disables the ship. I even gave it a value of 1,000,000 and every single EMP still disables the ship.
Original file:
ecm_strength = 82
Modded file:
ecm_strength = 1000000
EMP cannon has a strength of 32,
ecm_strength = 32 (from the file)
So why is it 100% of these get through and disable the ship?
Try changing the number to 500.
It will not give you 100% protection but it should reduce the number of times your ships are stunned
How would 500 help if 100 didn’t and 1,000,000 didn’t? 
Dunno - maybe 100 is not enough and 1,00,000 is to large for the game to know what to do with.
Apart from that I dont know what to suggest since it worked for me. I tested it in the Tutorial mission where the frigates are armed with EMP missiles. A fed cruiser was equipped with an advanced EMP shield and it was was effected less than when armed with a regular version.
I can vouch for my own test EMP Shield that I use to prevent the ships on the tutorial from locking down whatever cruiser I am testing; the EMP effectiveness drops to nothing. Here is the module in its entirety:
[code][config]
unlockcost = 0
lockable = 0
classname = “SIM_ECMShieldModule”
category = “DEFENSES”
size = “CRUISER”
name = “test_cruiser_ecm shield”
guiname = “Just Say No to EMP”
description = “EMP is disruptive to our tests. Shut it off.”
weight = 44
hitpoints = 55
cost = 80
icon = test_misc_module.dds
crew_required = 4
powerconsumed = 9
ecm_strength = 10000
slot_type = STANDARD
stack_effectiveness = 0.7
uisortpos = 2200
restricted = “test”
[dataitems]
0 = cost,DECIMAL
1 = weight,DECIMAL
2 = hitpoints,DECIMAL
3 = powerconsumed,DECIMAL
4 = crew_required,INTEGER
5 = ecm_strength,DECIMAL
[/code]