if it is pumping ink out of the system, and you can see ink going into the waste bucket, but the lines/dampers still have a lot of fluid in them, something is't working right. either the cap isn't sealing, the pump isn't working 100%, or the valved are sticking. something is making the ink not flow completely.
you can run the discharge and wash multiple times, if you're on newer firmware. it will ask you if you want to wash again, just tell it to do that, and it will restart the pumps.