I'm assuming that you posted the Call Lightning pic for comparison, and are not reporting some kind of trouble with that, too?
I don't have the code handy, but I do want to draw your attention to this sentence in the spell description:
Half of the damage caused by the spell is divine and the other half is fire-based.
This alone makes it very difficult to compare one to the other, since the 9d6 of damage (at level 9) would be divided between the two types, not 9d6 of Fire + 9d6 of divine. Add to that, each damage type apparently gets its own Reflex save, further reducing the damage done by half again, potentially. I noticed about half of the targets made their saves vs. divine where they all failed vs. fire.
I'll make sure that the dice are being rolled correctly when I get a chance, but just looking at your screen shot, the fire numbers seem reasonable. The divine numbers do seem a little low, but there may be some creature properties that account for that.
Because of how it splits damage, however, you should not see similar numbers as you do for Chain Lightning unless you add them up and account for potential halving due to saves. Even then, it could be the (bad) luck of the dice. 9d6 can produce anywhere from 9-54 points of damage. Worst case, with saves, it could do as low as 2-4 total damage (depending how NWN rounds) and as much as 27 points each for fire and divine. Median numbers will be more like 13-15 per damage type, which you're definitely seeing in the screen shots you posted.
Like I said, I'll look into the divine numbers to make sure there wasn't something goofy introduced by accident.