Oh dear, I hate to tell you this but we had *EXACTLY* the same spots and when I pu;led the vinyl back, the particle board underlayment was soaking wet and MOLDY. The grey was actually the MOLD showing through. You'll want to get that up and out of there as quickly as possible so it hopefully won't rot through the subfloor if it hasn't already. I think if we hadn't had 2"x5" tongue-n-groove fir planking for the subfloor, we would have been toast and had to pull out the subfloor as well.

The water very well could have come from the toilet but if you have particle board or OSB under your vinyl, the water can come from the corners by the tub/shower or wherever, it'll just wick it right up and then hold onto it.

Sorry to be the bearer of bad news.

Amy
Fremont, CA

Yikes! Thanks for the message. Guess we'll pull back the vinyl tonight and see what's under there.