If you've got water UNDER the floor, you've got a major problem...the floor it's sitting on might be all rotten (if it's wood). Before it leaked enough to pool, it could have been seeping - it could have been going on for a long time.
Is there any way you could take a look from below?
Sounds like the seal between the drain and the pan is leaking - could be a broken part, seal slipped out, or seal rotten, or something is loose.
I'm afraid to ensure the subfloor is solid, I'd want to remove it and then evaluate what's going on. This may entail removing the walls, too.