In my experience, 1D3 battery calibration can be finicky. I once calibrated it and it refused to go past 75% charge, still showing the "calibrate" message.
The battery may be on it's way out, but I'd try calibrating it a few more times anyways. If that fails, just use it like normal and throw it out if you notice you're not getting the longevity you get from a healthy battery. In the end, as Canon says, calibration is just so your 1D3 can continue to display the exact power left in the battery in the Batt. Info screen. I believe, though someone is welcome to correct me if I'm wrong, that the bars are still more or less accurate.
Sorry to be a broken record, but are you sure you're doing it correctly? I usually leave the battery for a long time and let it sit in the charger for a bit even after it's fully charged when calibrating, since I have had issues in the past with taking it out before calibration was finished.