Thanks for the additional information. There are some variables in your situation since you were unable to print a nozzle check with the CIS, and flushed the print head with PiezoFlush prior to installing the set of refill carts- but I will do my best to help!
Please remove the carts and examine the chip sensors in your cartridge carriage to make sure the thin sensor wires in these two positions look exactly the same as other positions, to make sure the sensors weren't damaged somehow when you removed the CIS. If the sensors all look the same and you don't see any bent or missing wires, I recommend you try different LM and BK chips- you can either remove chips from empty carts and transfer to the carts that contain ink (in place of the existing chips on those two carts, making sure to transfer the LM to LM and BK to BK, and securing the new chips using double sided tape), or insert a new/empty LM and BL carts just to check chip read without transferring the chips.
Please keep me posted- Dana