Well the same happened to me. I do believe it is more pathogen related. The worst reactions I got from B12 and selenium, but like you say it doesn't matter much what you take, vit C and E also gives out reactions.

This is also testable - take supplements that aim at detoxing waste products of bacterias, like ammonia. Among the most powerful are L-glutamine, L-ornithine and molybdenum. These supplements are powerful. In the beginning it is much more wise to focus on waste management, rather than stirring up more toxins that your body can't even handle well.