I have been checking our 3880 to try figuring out what's happening with your printer, and Wells just came in to tell me you just called with some additional information.
Please send me some photos showing the inside/top of your cartridge chambers, including the Y chamber in question, and neighboring LM channel for comparison. What I want to see is the chip sensors on the top/rear of the chamber. Please also send photos showing the top of your Epson Y cart, and if you still have it the top of the first Y refill cart.
Have you had this Epson Y cart installed the whole time, or have you ever removed/replaced it?
From my testing, and the update I just received from Wells, I'm curious if the Y chip sensor is damaged, which would cause what you're experiencing. I've never heard of or experienced a damaged chip sensor in this model, but have experience with it happening on other models. The sensors are made of very thin bent wire, and if the chip on a cartridge isn't flush or there's something sticking up on the cart, it can grab and damage the sensor when removing the cart (for example, if a cartridge was installed without a chip attached, it would most likely damage the sensor).
Please let me know, thanks~ Dana