Rose & Donald in Aurora, Ontario had a sewer back-up a while back. They cleaned up and then redecorated the basement, laying cushion flooring directly over the concrete. Now they have random spots coming through the vinyl that won't go away.
If good cleaning products can?t remove the spots, or stop them from coming back, I am afraid that there is contamination from the sewer back-up that has taken root in the cushion part of the vinyl flooring. If that is the case, there is nothing to do but to tear it all up.
Then the important thing to do is to be sure that the basement is not only cleaned up, but decontaminated. That takes a lot more than simply wiping a bit of bleach around. I recommend that anyone who has had a flood from surface water (as opposed to your own potable water supply pipes), or particularly a sewer back-up, should get copies of two publications from the Canada Mortgage and Housing Corporation (CMHC).
Cleaning Up Your House After A Flood
Cleaning Up Procedures for mould in Houses