There is no battery in these chips. The chips only reset with printing. They will only take 1 initial charge and that's it. After that they must be printed with to reset. That is the only way to reset an R3000 chip.
There are many reasons why battery chips are no longer available in the US anymore, but the big one was the import of batteries into this country.
One big thing that happens is people are not aware that a chip has reset. It will show as an error. They will turn the printer off, or replace the chip, and then it will show full again. It shows as an error when it has reset!!! But instead of topping the cartridge off, the cart goes back into the printer at a low level even though the chip has reset. So then air gets into the lines.
This is partly the reason why we just came out with a CISS for the P600. Too many people don't read instructions and get air in their lines on the R3000 because they let their chips reset without refilling carts. With a CISS, the cartridge in the printer is always full of ink and it's easy to see when the ink is low in the reservoir. When the ink gets low, you just top off by pouring more ink in. It's much more user friendly.
Long story short, you need to replace the chips that are too low for the initial fill to complete. Make sure all carts are full of ink before the initial fill process. Run the initial fill and it should re-prime your ink and get rid of air bubbles. Do not print with a partially air-blocked print-head!