Hi Rlzop2004,
Could it be that the transducer is not always submerged or surrounded by very turbulent water?
If the transducer is mounted to the stern and in a shallow location, are you 100% sure that it is not coming out of the water? (...due to pitching-motion of the kayak) Any kind of turbulence along the hull or turbulence in the wake behind your paddle strokes might also partially obstruct the sound-beam.
I am also using a Humminbird on my kayak, but I have the transducer and the GPS mounted on a rotating "pole", to the port side, just forward of my feet. When launching the kayak, the pole is rotated so the transducer is out of the water. I rotate it down when I am ready to record. When the pole is vertical, the transducer is deep and has a clear view to both sides of the hull.
If a stern-mount is the only option for you, I would try to mount it deeper.
Tore