Well, I doubt evaporation is the culprit, so you need to look elsewhere.
Not sure how much water was in the tank, but if it was leaking into the compartments, it would likely get out somewhere. Probably around the doors, or a vent hole, or something. I don't think any of the compartments are tight enough to hold back 50 or more gallons of water.
My first thought was to check to see if the fresh water pump is running when it shouldn't. A dripping sink or shower faucet, or a stuck open toilet valve (you did mention a puddle around the toilet), will cause the pump to operate and the water can simply be running into the waste tank.
Happy hunting. Let us know what you find.
'03 41' Friendship & 24' trailer with HIS '03 H-D Heritage Springer, HER '15 H-D Freewheeler Trike, and '08 Smart Car.
"Adventure is found in the journey, not the destination."