It ought to be related to your Destruction skill.
Why?

IMO neither archery nor enchanting affects the charge. Once the item is enchanted, it has a fixed charge that should run out in roughly the same number of uses every time. If you acquired the Nightingale Bow very early (<18 level), the enchantment is quite weak and doesn't last for many hits. I don't remember the exact numbers, but it was along the lines of 20-something.
Now if you enchant your own weapons, the magnitude of effect is calculated from your Enchanting skill and number of uses is calculated from the soulgem you use. Again, your weapon skill has nothing to do with it. Certain Destruction perks will affect the magnitude of elemental damage, but not the charge of an already enchanted weapon.