The partial_coverage option tells 3dAllineate to try to figure if the center of mass shifts between the two volumes have a difference that is much larger in one direction than the other over x,y and z directions. Each shift is evaluated in order of x,y,z. The direction is then ignored if it is more than double the shifts in the other directions. By having close to a full dataset, that shift was just on the edge of being detectable. Whether the center of mass shift is ignored or taken, 3dAllineate can still match the volumes as long as they are in the search area (translation and rotation limits), but an incorrect shift may move the volumes outside the search limits.

In the end, if you know the data is partial coronal data, it's best to use that option instead of the generic partial_coverage. Alternatively, you can increase the search area with the -giant_move option.