Hm, I tried dozens of Shield CE items, both vanilla and self-enchanted and both Shield and Elemental Shield and only a vanilla shield raised her AR. And, yes, I'm pretty sure I left the menu - but I can check again.
OK, I redid some testing, making sure I left the menu completely before checking - and I can't really see any logic in what works and what not:
WORKED:
Grand Ring of Aegis - Vanilla Ring - Shield
Escutcheon of Choroll - Vanilla Shield - Fortify Endurance
Self-enchanted modded dress - Shield
NOT WORKING:
Self-enchanted vanilla amulet - Shield
Robe of Defense - Vanilla Robe - Shield
Robe of Warding - As above.
Cape of Good Hope - Helmet from WarCry - Fortify Luck
Gauntlets of the Weaponmaster - Vanilla Gauntlets - Fortify Blade etc.
Putrid Hand's Master Robe - OOO Robe - Fortify Health etc.
Robe of Glib Tongues - Vanilla Robe - Fortify Personality etc.
Also, two oddities:
First time I stripped Vilja completely - and I noticed she has a ring on her right hand w/o anything in her inventory.
Self-enchanted modded gauntlets with Shield 12 gave her AR 3.
In short, most Fortify X/Shield CE items don't work, but some do - and I can't see any common denominator.