So last version seemed to fix this but then I got high enough CC rep to replace all my regular white Arrows. Seems to be working with regular ammo, but not with the green [Scout's Arrow] from the CC Rep vendor. Whenever I click auto sort it pulls all the ammo out of my quiver and sorts it into regular bag slots.
I'm thinking it might just be not reading this specific itemID as an Ammunition type?
Basically same behavior as earlier on TBC launch that was since fixed (for white Ammo)