I had a fairly similar problem to this. I bought a very low shutter count D6 ex-demo with battery [18c] & charger [Mh-26a]
There was charge in the battery so all was well but at first charge all was OK - at second charge the charger went into the alternating cycle of the charge [top] & then calibrate light flashing. No matter what I did I could not get it to stop this flashing, even when I turned off the charger & re started the charge cycle. Occasionally it started the charge cycle for a very few seconds before returning to the alternate flash cycle of charge & calibrate lights. The camera screen indicated that there was charge in the battery [2/3 to 3/4 full] and the battery life scale showed that only 1unit of the battery life has been used. With this info I assumed that the battery was "good".
I wasn't certain that I'd tried to calibrate the battery correctly, so I did as recommended and ensured that I pressed the calibrate button for a short while - no change! However I have eventually found a solution / work-around. With the charger turned on and battery out of the chamber, I pressed and held the calibrate button whilst pushing the battery into the chamber. The charge cycle began & completed. I will see if this has cured the problem long term or if I'll have to use this routine again.