Hi,
i use this config:

"Time before the loot containers are empties (seconds)": 20.0,
  "Empty the entire junkpile when automatically empty loot": true,
  "Empty the nearby loot when emptying junkpile": true,
  "Time before the junkpile are empties (seconds)": 30.0,   ​

30 seconds after i destroy a barrel of a junkpile, the whole junpile gets emptied and disapperas. Works perfect.
But this does not happen, when i loot a normal crate, or one of these toolbox crates (on the cars). This will not trigger the junkpile destroy.

Sorry, I can't reproduce the problem. Can you record the video?

same here, when looting a crate, junk stay, when destroy a barel, junk disappear