It is recommended routine maintenance to clean your capping station (even if it doesn't look dirty to you) once every 6 months. If it did look gummed up or there was accumulation of pigment around the outside rim of the capping station, you would have far more missing nozzles or completely blank channels all together. The function of your capping station is to create a seal around the head when it is going through a cleaning cycle, at the same time it sucks the ink away into the maintenance tank. There are tiny rubber tubes that transport the ink from the foam upper part of the capping station, then into the waste tank. What happens over time is the pigment starts building up inside the capping station in the foam area, as well as the rubber seal around the outside. Also the tubes start to build pigment inside and restrict the flow of the ink to the waste tank. If and when this happens, the capping station can no longer effectively move ink out of the print head any longer, causing clogging.
Another part to the system is the Damper assembly aka. Ink Selector Unit, this is comprised of all the Dampers, a ink selector for changing the black inks and the ink lines. The Dampers act as filters for your ink before entering the head. This replacement for the R3000 & 3800/3880 printers is becoming more and more practiced due to the age of these printers. This is a last line of defense if you cannot get the printer to give a good nozzle check performing the cleaning on the Capping station, Wiper Blade and bottom of print head video found here http://shopping.netsuite.com/s.nl/c.362672/sc.42/category.122444/.f
One more option is to install Flush cartridges after performing the cleaning in the video above and run an INIT FILL to flush the system entirely of pigment ink. If these 2 steps don't work, then the Ink Selector Unit will need to be replaced, at which point you will have an essentially like-new machine again.
Also, agitating the cartridges once a week is good practice to prevent settling pigments entering your system and clogging up your dampers. Go ahead and take each one out and give it a good shake and re-install. Clean the Capping Station, Wiper Blade and Print Head as instructed in the video. Run 2-3 Cleaning cycles and then the nozzle check. If there is no difference after these recommend procedures, then Flush carts will be your next step.
Let me know your results,