I see.

I think the engine must be located at the top of the main tank. Otherwise the water exhaust will have to be pumped up to refill the container - wasting any bouyancy energy you recover.

This might be where the problem is. The HHO generated at the bottom has to climb up to the top. It won't float up because there's no air flowing back into the container to displace it. The energy needed to 'pump' the entire containerful of water (in HHO form) up to the generator is no less than the energy you can recover from the bouyancy.