Re-equipping your bow fixes all piercing modifiers on arrows due to Sniper's Skill.  It used to be that every-time you finished an arrow stack you'd need to re-equip the bow, but I'm not sure if that's still the case.

Re-equipping the bow gives the piercing modifier, but i can't refresh or get rid of an old modifier anyway as i can see :s, newest arrow has +10, and an old arrow has +6, no matter how many times i re-equip the bow with the old stack.

At least in my game.

If the armor would be limiting, it would be 5 an 4, not 6 and 5.
But I tried taking the armor(dex mod limit 4) of and unequip->equip the bow a few times without getting the +6 i should have with 22dex(shortbow), but i get +5 piercing damage, as  i got unleveled with 20dex.

I poked around abit as i'm playing with the bowman atm, and noticed there's somekind of Weapon Specialization Proficiency feat for warrior and warblade, which gives them access to weapon specializations. I'm kinda noob at this editing, as i don't seem to get it into the bowman class, so, could anyone tell me where all places i need to edit for it to work ?

Edit: And btw, the weapon specializations are there, just one prereq (Weapon Specialization Proficiency) is missing from the bowman.