I was able to find this information, I'm taking information specific to other servers out of it, under the assumption that POTM did not make any changes to Shifter away from base NWN.
Item merge
Weapon is the primary weapon slot.
Items are both ring slots, amulet slot, cloak slot, boots slot, and belt slot.
Armor is the armor slot, shield slot (shield only, offhand weapons do not merge), and helmet slot.
The Gloves or Bracers Slot never merge in base NWN
Has a weapon? Merges all.
Unarmed, stands on two legs? Merges all (items and armor in base NWN)
Unarmed, four or more legs? Merges armor and primary weapon only (armor only in base NWN).
Exceptions to the rule are Death Slaad Lord, Stone Golem and Demonflesh Golem.
Did a bit more digging, and Amia devised a way to get everything to merge regardless, so it can be done. I'll take a look at some of the scripts/2das that are connected with the class when I get home and see if I can find out how to fix this.