Do you have any thoughts on why the gene expression of the non-responders was different than the responders group?

Genetic variations leading to a differing response to vitamin D supplementation is a previously identified phenomenon.

https://www.ncbi.nlm.nih.gov/pubmed/23935129

So that part isn't surprising, however as to why this genetic difference occurs between people? That I don't know. More information is probably out there in the literature that sheds some light on it somewhere. I haven't looked though.