Rodinal uses up the oxygen in the air and in the water, thus exhausting itself even if kept in an accordion bottle. As such, you should be using up what you mixed at the time - thus, mix up 500ml and use it and discard the rest. Mixing up 1500ml and using 500ml mean the 1000ml of the developer is rapidly losing strength, even sitting in an air tight bottle. This is unlike most standard developers - once the water is added, it should be used within hours, not days.

The picture is under-developed because the Rodinal did not have enough strength left to fully develop it. The Rodinal does not settle to the bottom, it just exhausts itself.