A Masterwork or Enchanted item loses the effects of Fragile (unless the item specifically says otherwise).
Since Fragile is (a) very long description and (b) PCGen's concatenation of descriptions is dire, we get things like:
+1 Vicious Great Terbutje
10 hp/inch, hardness 7, Fragile weapons and armor cannot take the beating that sturdier weapons can. A fragile weapon gains the broken condition if the wielder rolls a natural 1 on an attack roll with the weapon. If a fragile weapon is already broken, the roll of a natural 1 destroys it instead. Armor with the fragile quality falls apart when hit with heavy blows. If an attacker hits a creature wearing fragile armor with an attack roll of a natural 20 and confirms the critical hit (even if the creature is immune to critical hits), the armor gains the broken condition. If already broken, the armor is destroyed instead. Fragile armor is not broken or destroyed by critical threats that are not generated by natural 20s, so if a creature wielding a weapon with a 19-20 or 18-20 critical range scores a critical hit on the wearer of this armor with a roll of less than a natural 20, that critical hit has no chance to break or destroy the armor. Masterwork and magical fragile weapons and armor lack these flaws unless otherwise noted in the item description or the special material description, +2d6 damage to target, plus 1d6 damage to user
Note particularly the clumsy way it drifts from stating how Masterwork/magic negates all the text preceding, into the damage adds for Vicious.
It would be HUGELY improved if the data for Fragile defined that part of the text to be conditional on whether the item is masterwork or not (since all enchanted items are masterwork).
pathfinder core rulesets (or UE or UC)
Oddly enough, I'm not finding an Armor version of Fragile...
odd - it ought to be included, as PF added the fragile materials (bone, wood, stone,...) to both weapons AND armour... along with the Masterwork-and-Enchanted get out.