I'm having a similar issue right now. When our black tank is nearly full, water is visible on top of the tank. I cannot see where it is coming from, but I know it's not coming directly from the toilet. I will have to drop the black tank to repair it and I am not looking forward to that!
If you are seeing water on top of the tank, there's a slight chance it's the flange. The flange is mounted above the floor and only has the pipe going through. If you remove the toilet for an inspection, you will have to replace the flange anyway. It may be worth a look.