I've heard of that reaction from many who start low, and there is speculation that its worse the more deficient you are. I can't speak from experience, I started at 2.5mg day one, was up to 40mg within a week, and 100mg in about 6 weeks. I did have some flu like symptoms in the first few weeks but that was the worst initial detox.. I did have other detox symptoms for months, but nothing like what you describe.
There is also the issue of malabsorption, if that is a problem you have. It may be effecting your overall supplement synthesis... I hope some others chime in for you :)
Look into Weston A Price diet, make sure you are getting quality fats. This type of diet, along with about a year of supplementing has CHANGED my life, and I'm loving it.