I have the Fractured Winterglass with +1 Conjuration Mastery and no Masterwork applied, and the bonus is not applied.
I have a second the Fractured Winterglass with +2 Conjuration Mastery and Masterwork 4/12 and the bonus is not applied.
Update: I got an amulet with +2 to Conjuration today and tested it without tempering or masterwork and the bonus is not applied.
Update: I got Banished Lord’s Talisman and the +1 to core skills is applied.
It would seem that the issue is with conjuration bonuses in the amulet slot.