It could very well be mold. It looks to take on a grid like pattern just like joints in the subflooring. RIP up the edge and take a look.

I think Lisa G is right and it is following the lines of the sub flooring. Could it be glue? Mold makes sense in the living room because there WAS some water damage there at one time. But this is also happening in the first floor bedroom.

Carpet isn't glued down so I doubt it's glue. If you Google pictures of mold on carpet there are a lot that look just like yours in terms of coloring.