What might cause my liver and kidneys to not extract any vitamin d?

They do not extract. The liver and kidneys do not extract vitamin d, they activate it into forms that are usable by the body. Native vitamin d has no effect until it is activated. If your level is low it is because you are not getting enough or you are not absorbing it or you are not getting enough ultraviolet exposure from the sun.
See below. I am not quite sure what you mean by "extract vitamin d" from your liver and kidneys.