I posted this on the 40k thread. I should have thought about it and posted it here too.
Armor Locations for items should be one of the following for the auto equip to work. So, when creating an item use the following only in the "Protects" field. These are the only combinations that work, they mimic the rules.
Head
Body
Arms
Legs
Arms, Body, Legs
All
If you have layered armour and need the armor points to stack correctly, really the only thing you can do is create custom armour types to make it work. Say a Chain shirt layered over a Leather Jerkin, make a custom item "Layered Chain" and set it up from there.