The first thing that pops into my head when you mention that is "celiac diseases".
People with conditions like celiac disease, Gluten Sensitivity, IBS and Crohn's Disease will likely be Vitamin D Deficient unless they take large amounts of Vitamin D or get a lot of sun.
You will probably need a blood test,just to make sure.
2-Vitamin D is one of the fat soluble vitamins. That means that fat is required for it to be absorbed through the stomach,Simply take walnut or peanut butter or avocado or any other healthy fat when you take your Vit D3.
3-magnesium is required in order for Vitamin D to be converted into its active form in the blood. So if you are magnesium deficient then you will likely have difficulty converting the Vitamin D into a usable form in your body.
Hope this helps
Take care,
Bisan
I don't know but assuming your liver and kidney function is fine -- I'd ask about parathyroid issues. Perhaps someone else on this forum, who's been on D longer than I have, knows more about this.