I noticed that I'm getting way more loot than usual and it seems that the loot in the configs is being doubled and the loot from the built in defaults are being added to the chests as well. I'm using version 1.5.9 on 1.10.2.
Configs: https://github.com/belathus/Wanderlust-Renewed/tree/master/config/roguelike_dungeons/settings

After doing some testing, it seems that the pyramid and rogue dungeon files were somehow getting priority over the other dungeons so I removed them and everything works now

I think what's happening is that every time on startup, one of the dungeons get priority over the others and if I delete it, everything is fine but once I restart, another dungeon gets priority.

The problem appears to be caused by namespace collisions. When i change them, it works properly.