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Clicking alternated the grail + chest.. what is this about?

It does nothing except help you visualize things

Oh, that meant there was a Grail , Chest, Grail in that order?

nono, only 1 chest and 1 grail per level (as far as i know) 
the only thing you're adviced about is that the two obects are next to each other
either a way or another, to you to find out