Flawless magic doubles study totals for mastery abilities. Book learned adds +3 to the quality of a book that you read.
If magus Jim reads a quality 6 tractatus on a mastery ability does he get 18 xp or 15 xp?
18 xp comes from the quality of the book (6), +3 for book learner (9), doubled by flawless magic (18)
15 xp comes from the quality of the book (6), doubled by flawless magic (12), +3 for book learner (15)
I am inclined to go with the first interpretation (18xp)
What say you?
Reading the virtues suggests your interpretation. I'd house rule it, though, To be excluded. Using your example it would be 15 xp. Flawless Magic is, IMO, the most powerful virtue in the game. Allowing the Book Learner xp to double, more so.
I would go with the first interpretation.
Elementalist and affinity makes for a fun set of combos also.
Affinity Ignem
Affinity Auram
Elemental Magic
What's that? When I gain 6 XP in ignem, Affinity knocks it up to 8 ( multiplies by 1.5) which means that my elemental magic carries that over to Aquam and Terram. My Auram gain multiplies the 8 by 1.5 for it's affinity and knocks that up to 12 
Of course, that's using an interpretation of the rules that is designed to Munchkin.
Huh? You only get one additional experience point per Art when you put at least one XP into one of the Elemental Forms. So, you could put an XP in terram and get two in Ignem and Auram and one in Aquam.
And I think it's a good thing to assume that affinity never double experience points (even if it does by RAW) else all hell breaks loose 
I much prefer the MetaCreator implementation of affinities, which doesn't increase experience points by half, but instead lowers the level at which an ability score is earned by 1/3.
And in another saga I'm in, where the SG doesn't use MetaCreator, tracks the raw or earned experience points and then multiplies them to determine the derived value.
That sure is a good way of doing things.
Affinity specifically says that it rounds up not down so by that interpretation you get 9 in auram here.
The only time that affinity would realistically double xp gain is when the character only gets one xp in a season. I don't see how that is ever going to break hell all of the way loose.
I dislike metacreator for that. It's conceptually sloppier than the book and it doesn't work as well with gaining and loosing virtues in play.
Easy:
Flawless Magic doubles Study Totals.
Study Totals are derived from Quality (usually via := but that's secondary).
Book Learner adds to Quality.
If Book Learner had added to study totals, there might have beena question, but as it adds to effective Quality, it's not terribly complicated. 18 XPs, like it or not.
I' ll grant that it could be better, especially with respect to adding and losing affinities in play. But if it's such a problem, ask for a change. I reported the Flawless Magic errata to the developer and he changed it so that it properly doubled all experience.
Wanted to add that I really detest the rounding gimmick that happens with 1xp becoming 2, as well. Tracking total XP and then multiplying them to determine whether the total meets or exceeds the level for an ability score is the best method, IMO.
Which is why I, personally, prefer to track the fractions. So 1.5 xp is just recorded as exactly as that.
I really like this idea.
So much hate for the extra half an experience point per season. My tastes in this particular issue are diametrically opposed. Let the players have an extra half of an xp. Let them do it twice if they split their exposure between two arts/abilities where they have affinities in both. The players will enjoy it, and compared to the impact of more or fewer free seasons of study quality 8 versus quality 12 tractatus and the availability of vis it makes precious little difference.
Tell me why you dislike it so much.
I'll admit it's not entirely rational. Tracking the base experience points and multiplying it to compare against the advancement table, and tracking fractional experience points solve the issue, though.
Over the grand lifetime of a magus, the extra experience point adds a lot, especially if they are putting into to Arts/Abilities with affinities. Adventure XP gets allocated to the art/ability with the affinity and it's always odd, so as to get the extra experience point. It's a bit of a temptation that even good players who don't go full munchkin are going to find hard to avoid.
Same as Mr Link here 
I am interested that Jonathan.Link thinks Flawless magic is the most powerful virtue in the game. I really like it but I've been strongly conflicted on whether it is actually worth a major virtue.
Having just created a character with It I can confirmed that for many of his spells, mastery is entirely irrelevant. They don't need the casting boost, don't need penetration and usually end up with abilities like still or quiet casting just to make the PC look flash when casting. He certainly won't be increasing his mastery score on them.
I can clearly see the use when mastering attack spells or those that need penetration, its useful with rituals too. But most characters I have played have few of these and a PC might be better served taking the mastered spells virtue (bonus, only a minor virtue rather than flawless' major) for the 50 xp in spell masteries.
My games have never had too much in the way of books on mastery lying around which might well colour my interpretations. I do recognise the use of doubling practice experience as it means you get mastery 2 in a spell with only one season of study.
Has anyone else played a flawless magi and can they relate their own views?
I know you asked about others' experiences, but I thought I'd add my two bits.
All of your spells get a +1 CS bonus automatically, and all get one less botch die than normal, again automatically. For the equivalent of 5 xp you double the benefits I mentioned.
Agreed, certain spells it's a bit harder to make the case. I'd be interested to see a sample of these spells though. With rituals, the mastery skill isn't always useful, but removing one or two botch die is, especially as it comes after things like the Golden Cord and Cautious Sorcerer.
50 xp of mastery goes quick. Why not make it 100 with Flawless Magic! 
But yes, combat gets a lot of attention from mastery abilities. Still, there are other good ways to use mastery abilities other than combat.
I have a character who has Flawless and Subtle Magic, a lot of his spells have quiet casting taken at least once, a couple I think are taken twice, like Prying Eyes. This gives him a lot of advantages of casting spells when others don't know that he's casting spells. I know that one could get the same benefit of still and quiet castingx2 with Deft Form, but of course that only works with one specific form. I had some general feeling when I built him that I was going to turn this character into a generalist, because I normally don't play a generalist. Now, he is an apprentice in a saga where the PCs started as apprentices in Doctorcomic's Alpine Apprentice saga, and given the house rules in that saga he has a lot of spells, 230 some levels of spells (we are near the end of the apprenticeship). I kind of see him as a MacGyver type but with spells for any and every occasion.
Fast casting (defensive) spells also becomes a bit easier, because the fatigue loss isn't a forgone conclusion when a spell is mastered for fast casting as it would be for a spontaneous spell.
In the thread I started about the average quality of a tractatus, and we got into discussing how many there were in existance, I posited that there would be a lot of Spell Mastery texts out there, especially combat related spell, and any useful ritual spell will have them, too. Depending on how many texts you think exist, I think it's reasonable a lot of even low quality level of texts for mastery exist, just because it's so useful and vital for minimizing botch dice.
Edit:
Wanted to add that my experience is that it seems to mesh well, if not magnify, a lot of other Hermetic Virtues when placed on a character. Which clearly it does in the case of your original post.
My views...
Double the xp gain from the book, so 6xp +3 equals 9, doubled equals 18.
I have never used Metacreator. Pen and paper and calculator. Or a text document, I am modernized I suppose :mrgreen:
But I run into players that use it all the time and from what I have seen, it is a confusing mess.
And Flawless Magic is not so super-powered at all. It is useful for a couple of spells, but not every spell. And it sorta sends you down the path of collecting a wide variety of generic spells just so you can get your money's worth out of the thing. It makes your specialization "spells" rather than any one Art or Focus.
Which is not such a bad thing now that I think of it.
What if Flawless Magic was a Minor Virtue, but also inhibited your ability to make magic items? Halve Lab Totals for Charged, Lesser, and Invested Items?
It gets a bit messy when a character initiates the affinity virtue or looses it in an initiation.
I'd imagine you'd want to determine the score prior to the virtue change and translate it into an equivalent value to be used afterwards. The alternative - I had 100 xp in penetration now I have 150 yipee! - or -I had a magic theory score of 7 now its down to five darn- don't match with my vision of what the virtue means.
I see the virtue as meaning that you pick up the skill more quickly than others. The character's mind is more attuned to assimilating information about that subject. (Puisant on the other hand means that you perform beyond your knowledge.) The extra xp gained per study period maps satisfyingly on my model of what the virtue means in the story.
This is true I guess I just don't see the extra experience point as somehow unearned or cheap. Affinity is a virtue that they paid for, they should get the rewards (I'll admit that it's a fairly strong virtue). If I did I might share your feelings for the different xp scales option (or Arthur's amazingly simple "don't round the xp total" idea).
As someone who is bothered by (ok this is a guess you may not really be bothered) the munchkinness of the round up rule, do you see any benefits for the metacreator "solution" that aren't achieved by Arthur's method?
My understanding is that metacreator originally sprung from a Hero system tool that was applied to other game systems. Hero system's philosophy is to attempt to make a build point worth the same amount of utility no matter how it is spent, so a 600 build point character is balanced with any other 600 build point character. This set up is ingrained enough in the assumptions of the software that it was hard to make it do affinities the way that fifth edition described them. It wasn't an attempt to "solve" anything perceived to be a flaw in Ars Magica (This could be completely wrong I've no sources for it.)