If you like, send me an e-mail with your savegame to warhound°support{Ã┼)hispeed°ch so i could take myself a vague look what is wrong. However remind maybe, there is no toolkit for v2.3/addon so it's usually quite complicated to trace bugs there.

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Edit:

I've made a quick test this morning visiting the Vault of Therayne in mercenary mode, and i was able to activate/deactivate all stones resp. light beams from the first until the third quest. Also these quests seemed to react/trigger well, liberating Meraliss (F&K) and the caught monster boss was possible (while solving the third quest was too tricky *cough*).

Now this doesn't mean there are no bugs. As recent issues have shown, problems sometimes only appear in veteran or elite mode (for no evident reason), sadly i had no appropriate savegame to check out these quests in the these modes too.

Actually there is a knwon bug within the revised auto-casting AI affecting the 'Steal Magic' curse, so better try to avoid this spell currently (will be fixed in Alpha 2r).
Generally, the longer you play, the more probable is it that matters appear. So i recommend to do these quests as soon as possible after game start. As you know probably, the closest teleporter station is 'Western Vai'lutra Forest (North)', then just walk back southwards, the world map should show you the Vault entrance on the left/eastern side of the canyon/forest.