Vitamin D and Magnisum defeciency.

I have been suffering from joint pain  in both knee especially in nights for more than a year and checked many physicians for this and took also advised to took lot of blood samples  RA test came normal and lot more blood test finally took vitamin D3 on four months back came around 17 with magnesium level 2.18 and suggestions to take vit d 60k for weekly once and remmeg 400mg for three months so i continued almost two months later felt somewhat better but had knee pain quite often and then last month i checked my vit d level it came 46 around and suggested to continue remmeg with  folvite mb daily once this time and said my megnisum level is getting down thats why paining so i took one day but my pain gets worse than before ... Do i get affecting due to these medicines shall i take magnesium tab for long and do i continue this medicine please guide to recover from these its killing everyday