Is the rot on top, bottom?
I ditto on the shower/toilet. Have you checked the existing toilet flange?
If the connection between the toilet and the black tank has come loose or is cracked, every time you flush the water can spew out possibly getting the underlayment wet and pooling on the tank itself. Best bet is to crawl underneath, remove the underbelly material - coroplast?, inspect the tank for pooling and then check your connections. Have someone flush the toilet, run the shower, etc. . Hope that helps.