What about the airspace in the hull?
The sound waves don't like travelling from one medium to another. Idealy they get hung over the back of your boat and covered in water. If you place the transducer inside your hull and press it against the bottom there is still an air gap which will upset the transmission of the sound wave.
To overcome this the transducer can be stuck down with "goop" such as "Marine Goop" or "Selleys All Clear". Some people also build a small "dam" out of foam and fill it with water. The idea is to exclude air and make the transmission path look more like water.
More info can be found on the kayak fishing forums or here-