SPOILERS AHEAD - anyone who has not completed the game should not read this post
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When exactly are you casting the Detect Evil?
The failure of Detect Evil to work prior to finishing Dragon's Eye has nothing to do with the spell. As I understand it, the real Arundel (who is not evil) is always attacked while your party is in transit back to Kuldahar after killing Yxunomei. The presence of neo-orogs in Kuldahar is the clue that the Arundel you meet on the bottom floor of the tree dwelling is false. iirc, he talks to you as soon as you enter, making it impossible for you to cast Detect Evil before the conversation starts.
If you cast Detect Evil before the conversation starts after killing Yx, just ignore what I just said and continue your speculations.
It only makes sense that a being of sufficient power could prevent the operation of a low-level divination spell. In 2nd AD&D, there are two low level wizard spells that can block the detection spell, although neither is a spell in the IWD game; Misdirection (2nd lvl) and Delude (3rd lvl). I would assume that the 8th lvl spell Mind Blank, which is a spell in the IWD game, is also capable of preventing this divination.