My 9900 was not recognizing several carts last week and Epson tech support was of no help whatsoever. They thought it was the main control board and scheduled a service technician to come out. He was in the area last Thursday and dropped by to check things out. When the parts showed up this afternoon, he returned, and in the meantime had been thinking about the error code I had reported to Epson.
Turns out that these carts are very similar to the 11880 carts and those printers have had some issues with internal air pockets tricking the printer into thinking it's empty. He popped out the yellow cart which was not registering, and with the label side up, gave it a couple of knocks on a hard table, followed by a gentle shaking. Bingo. Everything is fine again.
It's too much to expect (even if it shouldn't be) tech support to think outside the box, but not apparently for a great independent technician. Hats off to Pete Hoeffner.