Ok , these are either Major/Minor or Minor only (page 39 , ArM 05).
I was under the delusion that taking the Minor version gave it to you at a value of +03 ,
and that taking the Major version gave a value of +06.
Personality Traits (page 18):
Is there a section in the RAW that i have been missing all these years regarding this?
Realms of Power Infernal and The Church both state when discussing personality traits that a Major Personality Flaw is equivelent to a +6 personality trait while a Minor Personality Flaw is equivelent to a +3. However, the section on Personality Flaws in the core rulebook does not share this. It instead states the the difference between Major and Minor Personality Flaws are that Major Personality Flaws get you involved in adventures, while Minor ones just color the character.
Minor i give +-4, Major +-6 and Greater +-8. That means a minor can generally be overcome fairly easy if need be while a major can be troublesome and a greater personality flaw will usually take a lot of time or effort to deal with.
Though i generally step the description to "one level worse" as i think the descriptions are often far too severely damaging to the character as written while others are just character "colour". Temperate for example can be played perfectly fine without ever causing even the slightest problem while Prohibition, Non Combatant or Judged Unfairly among many others can be severely limiting or problematic.
I try to stick with description of personality traits flaws:
major are mandatory for roleplaying. If you can play a major personality trait, you have to, but can roll against if needed. For that purpose, I use a value of +6 which is hinted in ROP I
minor are coloring roleplay. So they have no value as such, but the player can take those at value +1 to +3 like any personality traits he could take without flaw
I think yours is a case of legacy rules. In 3rd edition it was as you mention, and it might be that in ArM4 it was like that as well, even if they were not called minor/major back then.
Cheers,
Xavi
"Personality Traits area short description of important features of your character personality. For major characters, such as magi and companions, they should be nothing more that an aide memoire, and a reason to think about the character's personality during character creation." (AM5, p.18)
So really, if a magus has a Major Personality flaw, it does not really matter what number you give it as a Personality Trait, because he shouldn't roll them to begin with, he should roleplay them. As has already been mentioned, if it's a Major Personality flaw, then the character will act on it even to his detriment, with no roll required; and if it is a Minor one, then the character is expected to roleplay it but it is not overriding, at most in a difficult circumstance he may have to spend a Confidence point to ignore it; once again, there should be no roll involved.
And if the character is a grog, he is expected to go with his flaws even if it means his death, because that's what grogs are for 
And for when that is unsuitable or the character has contradicting motives, the number can be VERY useful.
It's worth checking out the sample characters early on in ArM5 pgs 26-27, where they lay out exemplar magi for beginers.
Here, only Major flaws occupy one of the character trait slots, at +/- 3 apiece. Minor flaws are not repeated as traits.
From this I gather that only Major flaws should regularily require roles, whereas Minor flaws should drive motivation, but be possible to overcome in specific situations.
For example: Wrathful (Major) v. Wrathful (minor) in situation where wrath is provoked. Major flaw must roll to prevent self from lashing out, then and there, possibly with violence. Minor wrathful simply feels really angry, but holds his tongue. His character becomes short with the target, and may be seeking payback down the road.
If it is a minor personality flaw, IMS a wrathful character would strike a blow in the face on the offender, or let out a sharp and extremely offensive retort, and be ready to retailiate (probably with violence) if the offender does not back away.
The major wrathful dude would simply draw his sword and attack.
Never seen back to the future, or what? 
Xavi
But this is untrue if you read a little more. The very first character (page 21) has Angry +3 and Wrathful (minor), which itself says "you are prone to anger." Also, Reckless is minor and explicitly says you get the Personality Trait Reckless +3.
Chris
The way I've played this is:
Personality trait without flaw: this is roleplaying color for a character. In most cases it won't come up except as a second-hand event.
Personality minor flaw: in terms of roleplaying this isn't significantly different to the 'no flaw' variety, except it should be a fairly big part of the character's personality. By taking it as a flaw the player is also saying 'and I want this to show up more frequently as an issue in stories'. So personality flaws of characters get tested more, and in some cases get rolled against for extreme situations.
Personality major flaw: in terms of roleplaying this is a central feature of the character's personality. If a situation arises that would prompt response based on this personality, the character -must- respond to it. This is true even if it seems like a bad idea. Confidence can be spent to resist the temptation of the flaw - to prevent doom-by-obvious-trap for a major character should the situation arise.
As for values: minor flaws get +3, major flaws get either +3 or +4 depending. This only comes into play in situations where the value is actually needed - such as a person with the major flaw 'compassionate' being mind-controlled to kill someone.
See Ars p37.
From what I gather: