When you right click the crate with the wrench, and then put the crate down again, it gives you the amount of items back into your inventory, but also keeps the amount of items in the chest, so you get the amount of what you got in your chest 2 times back. I'm currently running the 1.0.11 voltz server, and i have no clue of how to fix it.

By the sound of it being 1.0.11 voltz i guess its out of date knowing that there is no recent version. As well as far as i remember i fixed this issue already and have not seen it repeat.