Water is def not a renewal resource. That's why it illegal to use some places. There is probably something leaching into your tank. I doubt the roof would have anything to do with it unless something was sprayed on it even then the rain water only touched it for at the most 3 seconds.
Google search for a water supply store say culligan man if in Ontario. Call them out to have your tap water tested they will test your rain water too
I use rain water for my dwc but I add cal mag obviously my water tested pH of 6.8 and ppm of 8.
Unless your in a heavily populated and polluted city like LA where acid rain could be the problem (not sure about alkaline rain tho).
Have you considered a possible microb problem? That would be my first place I'd start. Some how sterilize your holding tank with
hydroguard or enzyme complete even high dose of h202.