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That's interesting. You could place the better enchant on the off-hand weapon, and craft it with the Charged (Amethyst) trait. Perhaps that would turn this into an advantage. Oh, and use the Dual Wield Expert passive to boost off-hand damage.
Don't you only hit with your offhand when doing Heavy attacks? I assumed my main hand hit on light/partials but both hit on heavy attacks. I would hate for my light attacks to be going off my off hand since it's weaker.
Might also be that your main hand hits harder and therefore deals the killing blow more often than your off hand. Meaning that as long as it strikes first, it will often be the last hit on a mob meaning it will drain that much faster than the main hand.
"As an online discussion of Tamrielic Lore grows longer, the probability of someone blaming a Dragon Break approaches 1." -- Sheds' Law
Have you seen the Twin Lamps?
This could be a shot in the dark here, but is it possible that one enchantment is simply proccing more often than the other and thus draining quicker? Enchantments do have internal cooldowns and some are a bit longer than others.