Actually the implication is that the throne was made of orichalcum. Starswirl later uses some enchanter fragments of that throne to create an anti-teleportation ward around the castle in canterlot.
Assuming the throne IS made of orichalcum, then it probably means that either the changelings adapted to it (not impossible. they're CHANGELING, changing themselves to work around the orichalcum doesn't sound impossible), or they found out a way to enchant/modify the orichalcum so it wouldn't affect them.