It doesn't sound like water seepage. Water doesn't behave like that - in isolated spots.
You need to take a picture of this and post it.
Could the stains be mold? Dampness and darkness would make it appear on the surface. Light and drying out would make it recede below surface. I doubt, though, that you'd mistake mold for a liquid stain...
Another way to refute the theory that it's water seepage is to lay some clear polyethylene down in a large square. Tape the edges sealed. If you get no condensation after a few days, then you don't have moisture seeping through the slab.