Follow this procedure exactly, in the order given here (I'm assuming you don't have the wall charger connected):
Fully power off your headset (not standby mode).
Disconnect the Elite battery cable from the headset.
Plug the Elite Battery back into the headset.
If the LED on the Elite battery is lit, wait until it goes off.
Press and hold the button on the Elite battery until its LED turns green. Keep holding the button but release it immediately when the green LED goes out. If the LED has started blinking orange, you held the button too long, try again.
Briefly press the power button on the headset and put the headset on. Check that it shows both batteries in the eyepiece.
Power up the headset, the batteries should be working correctly now.
Note: I find that it is mandatory to power off the headset before unplugging or connecting any of the cables, otherwise the charging or battery consumption does not work as expected (ie. evenly distributed across both batteries).