the 1D3 battery has a 3S LIC 18650 cell battery pack. if you're getting a recalibrate message it's likely that of te 3 cells, one or more are out of balance. i.e when charging and discharging are done they don't quite reach full charge at the same time, and cell balancing is needed. that's what the message is for.
the typial full charge voltage of a lithium cell is 4.2V, and cutoff is sometimes 4.25V and then the voltage drops back to 4.2 fairly quickly. so it could be that maybe cell 1 has reached 4.2V when cell 2 and 3 are still at 4.13V for example. the diference is small but it's enough to require calibration. if you have a faulty or damaged cell, then maybe two of the cells will get to 4.25 while the third lags behind badly. i'd say if you can't tell, bring the battery back (if it's still under warranty) to canon and just ask for a replacement.
How old is the battery? if it's done about 30-50 cycles it may take a few cycles to balance the cells. it's quite normal to take a few cycles to really balance and calibrate, but if say you cycle it 5-10 times and it still gives this message you pretty much can conclude that one of the cells in the battery pack is not working right.
i'd put the battery in your camera and drain it real quick, like set it to manual sensor cleaning mode or Using IS a lot. then cycle it till you're sure that battery pack has a damaged cell.