Have you tried to replace the 9V battery for a new one?
Or maybe some issues with your cables or the output jack of your bass?
Got an active Ibanez and Sandberg bass, both 5 string and they work fine with the dwarf so far.
Your tests seem quite extensive and if reducing the input gain together with an empty pedalboard doesn’t help I’d suspect some issues other than the Dwarf.
Also, the input LED of your Dwarf isn‘t red when you hit the B string, is it?