I have been stuck on step 4 of 22 of act 3 of Echoes with no hope of it working. I still have the marker on the Nessus map and the marker is sitting where the box should be, but when I get there, there's nothing to interact with.
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That's the persistent room marker to tell you its in that room, you already picked up the box that was next to it. Recheck the room carefully - this video shows all 5 locations: https://www.youtube.com/watch?v=6XmB6OHIeMo