It must take a very long time ;). Maybe because the laser scan is huge, or because the difference of coverage is too important. It's hard to see that on the snapshot. Can you maybe crop the clouds so that they have more or less the same coverage before computing the distances?
EDIT: Oh, I see that their are only 15 cells, which means a very low octree level. If it's not because of the relative coverage, then you'll have to set it yourself (try something between 7 for small clouds, up to 9 or 10 for large ones).