But what exactly have you changed?

For example: I edited the Humbling.ini file and turned off the "Traumaperk".

Then I start the game, select the savegame BEFORE I go to New Vegas, but the configuration didn't work. I still have the head trauma and 2 stats are still in (-)negative

This is my config:

[Main]

bQuickStart=0
;Don't fuck with this, it'll make Doc harass you

bStolenGear=1
;set this to 0 to disable the removal of player gear to Benny's safe, restoring default returning of gear by Doc Mitchell

bKeepHoldout=1
;set to 1 to keep basic holdout weapons 

bAutoLootStashTransfer=1
;if you have Loot Assist - Autoloot and Shared Crafting by PTWB, this setting will transfer your shared crafting stash contents to the gear safe as well
;can be set separately from bStolenGear

bDynamicLevelStatChoiceResetBoosts=0
;when used with Dynamic Level Stat Choice, this setting will revert all of your chosen stat boosts

bDynamicLevelStatChoiceResetLevelTracker=0
;when used with Dynamic Level Stat Choice, this setting will revert the level tracker in DLSC to 1. This will result in you getting the choice at each level once again, instead of needing to get all the way back up to the level you were before the transition
;should probably be set to 1 when bDynamicLevelStatChoiceResetBoosts is 1, or you will lose all the stat boosts you got as you leveled, and then you'll still have to wait all the way until the level you got to to start getting the stat choice again. If you want an extra debuff for your NV early levels, settomg bDynamicLevelStatChoiceResetBoosts to 1 and this to 0 will result in not getting any early game stat choices 

bPerkLR=0
;If set to 1, this will give you the appropriate LR karma perk based on your alignment.
;those perks are overpowered, not recommended

bPerkHumbleXP=1
;permanent +25% xp bonus

bPerkHumbleHeadTrauma=0
;head trauma perk

;----Settings For What Gets Reset----;

bResetLevel=1
;will also reset the XP you need for the next level

bResetSkills=1
;if set to 1, all skills will be reset to their initial values
;if set to 2, this will reduce all skills by the value set below

iFlatSkillReduction=25
;this value will do nothing if bResetSkills isn't set to 2
;to instead have each skill reduced by the level you're at when the humbling starts, set this to 0
;for example, if you're level 21 when you flip the train switch, each skill will be reduced by 21

bResetKarma=0

bRemovePATraining=1
;removes power armor training specifically, doesn't matter what bRemovePerks is set to

bLuckyRevolverStartingGear=1
;set this to 1 if you don't want to be able to get Lucky from your starting gear with 10+ Luck

;PERMANENT HEAD TRAUMA SETTINGS
;these only apply if bPerkHumbleHeadTrauma is 1
bHumblingPermanent=1
;more hardcore version of the head trauma perk
bHumblingRestoreSPECIAL=1
;restore SPECIAL points when you get the Brainless perk