because yellow is at the tail end of the capping station. that lends me to believe that you may have your caps misaligned and the yellow is camming up higher than the balance of the capping station. paint the edges of your caps with black ink. now park the heads on the caps. pull the carriage to the side/left and with a flash light look at the bottom heads. do you see good clean imprints of the caps making centered contact with the heads? or do you see outlines that are broken, missing, or sitting on the SS edge of the head platen?
you may need to shim the front side of your capping station, or stretch its internal springs out just a bit to get more upward force.
one other thing to try is when you are doing the ink fill, push up on the bottom of the capping station to compress it up against the heads. does this help pull ink or no help? make sure if you think you do have mysterious air leak to get an automotive stethoscope to listen for air (pull a vacuum at the waste line and listen for the hiss).
also, if you pour cleaning solution down the caps, does it disappear. a common place for a clog is right beneath the caps.
good luck and keep us posted. there are a lot of jv3 veterans on this board that have been through what you are just now encountering for years. mikepro, and many others know these machines really well.