Did you check right behind the spot you teleport in on? When we first started doing Limbus we were relying on the JP maps that were out there (and referenced on the wiki now), and this time chest pop location was unmarked. So for a couple of runs we would occasionally get boned by thinking we didn't get a time box for that floor.
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As for the Armory weapon, it showed up as an NPC?

In our runs we tried attacking it one run before we had killed all the other weapons on accident. The ninja that hit it had his melee hits do 0 damage, and consequently the boss didn't aggro him; it just hung around chilling on his little platform.