I just fixed a similar issue on my JV-3 last week.
It was the cartridge sensor. It is a small lever at the bottom of the cartridge well. If you look at the side of your cartridge, with the chip on the upper left, you will see a small rectangular hole (approx 1" x .125") at the bottom. This is where the cartridge sensor on the inside of the cartridge well matches up with your cartridge. I believe the part number is Mimaki 1033477. ALthough, check with your supplier to make sure it's the right one for your machine.
The sensor has a small plastic lever that is easily broken or even hairline fractured which will effect how it read the cartridge. Once it reads it as "near end" it will write that information to the cartridge chip.
A tech told me it was an easy fix, but I beg to differ. It was A LOT of taking apart. I did it though. So, if you are not too afraid, you could probably do it. i would guess it took me about 3 hours. Mine was a magenta. Supposedly, Cyan and Yellow are much more difficult because they are behind the carriage assembly area. -MM