Suppose you could be getting some cross contamination. This happened to me once or twice when the hose broke inside the pump. The pump is a crappy design. I kept extras around and some R/C car fuel line to repair it when needed. The hose will walk toward the white gear. The gear will eat the hose.
One quick way to test is to running a cleaning cycle and check to see if you are getting movement/bubbles or something out of the two small drain lines going into the waste tank.
Also, during the cleaning cycle, watch to make sure the wiper extends all the way out and wipes the bottom of the head. If it's only cleaning a portion of the head it could cause ink build up and you could loose suction on your capping station.
Just a couple quick thoughts.