Causes for Vitamin Deficiency

I'm wondering if anyone might have any experience with vitamin deficiency...
I was diagnosed last year with hypothyroidism. I'm now on levothyroxine 37.5mcg daily. After beginning treatment, I noticed some severe cramping in my hands, feet and legs. I was checked earlier this year and found to be Vitamin D deficient. I believe my level was at 21. When I went back to see my Endo two weeks ago she did the two "tests" for Calcium defienciency. Not sure of the spelling, but it was something like Chzoveks Sign and Thousseaux Sign. They were both positive. I've been on 50,000 IUs of Vitamin D 1x every 2 weeks for 6 weeks now and I started Calcium 600 units a day about a week and a half ago. In addition I take a multi vitamin which I've been taking for a few months now.

The problem is, I haven't seen any change in the cramping at all. It's horrible. I thought the bone in my toe was going to break yesterday because of the way my toe contorted with the cramp!

Is there any reason why I wouldn't be absorbing the vitamins the way i should be?? I am 33 years old, not menopausal and have asthma, GERD and Hypothyroidism. I am overweight (about 80lbs) and am looking at getting weight loss surgery. I want to be as healthy as possible going into this experience so I don't have MORE problems.

Any help would be appreciated.