God is more interested in your character than your comfort. God is more interested in making your life holy than He is in making your life happy.
God doesn't owe us an explanation for everything and actually what I've found is that explanations don't comfort. What comforts is the presence of God, not the explanation of God.
Nothing works perfectly. The weather doesn't work perfectly. Because of sin in the world, nothing works perfectly. But in spite of that we can find comfort. We can find strength.
Explanations don't comfort. You won't feel better if you know why. It won't hurt any less.
If you always feel comfortable reading God's Word, you're either not reading ALL of it, or you aren't letting it sink in.