Can you attach a syringe to the capping station and draw the syringe and listen for air leak. If you get resistance and ink in the syringe the caps are set fine.
Also is the drain line from the pump clear and unblocked? By putting some cleaning fluid in the syringe and attach it to the drain pump line you should be able to force some fluid out into the drain bottle. Do both lines or however many there are on your unit.
I also one time had the little rectangle shape thing with a spring (it pushes against the capping station to seal two small rubber nibs that have clear tubes that lead to the capping station) anyway this came off and when the capping station was set in place, the nibs were not covered by this plastic rectange and there was an air leak and the pump ran but could not suck anything due to the air leak.
