A pumping apparatus for use with a pump set to deliver fluid through the pump set to a subject includes a pumping device capable of acting on the pump set to produce a fluid flow within the pump set. A controller is in communication with the pumping device for controlling operation of the pumping device in a feeding configuration and in a flushing configuration. The controller is adapted to store a selected flow rate and a desired fluid volume of a first fluid in the memory and at least one of a flush rate and flush volume of a second fluid. A flush time compensator is capable of being run for determining a compensated feeding configuration of the first fluid based on an amount of time the controller will operate the pump device in the flushing configuration and the desired fluid volume of the first fluid.
