I am not surprised at all. I am a big proponent of vitamin d and there are many many studies that draw direct correlations between vitamin d deficiency and auto immune disease.
I had very low vitamin d and have been supplementing since May. I go next week to see the results of my blood tests this week (Vit D, Thyroid, ANA, Sed Rate, c-reactive protein, liver enzymes, iron...blah, blah, blah...).
I hope the supplementation helps you feel better!