Whatever is getting in your system/s may be in your water source to begin with. Weather directly out of the tap, or any storage containers used to put it in. You mentioned that your getting the same smell from your seedlings, so I would wonder why. And the water would be a common thread between them. Pathogens and fungi spores can still make it through a water treatment plant. Even airborne spores could be getting into your water after you get it from the tap.
I don't think you have any plants in the main system yet, so I don't think you were using
nutrients in it yet either (until now), but rather just plain water for testing it. I assume since your seedlings are still real small, your probably not using nutrients their either. Or at least a very diluted amount. So there must be a common thread between your main system and seedling propagation tray if they both are having the same issue.