You might want to read this thread
for some possible reasons for the lack of arches. Some of the explanations they give are that the lines might not be fish (air bubbles instead) or the fish could be moving.
I use a transducer arm too and have had the same problem but not as bad as yours sounds. I try to adjust everything as best as I can before I get underway and if I have to make adjustments on the water, I make sure to loosen the clamp a lot to prevent the ball from moving when I move the arm. Once I tighten it down, it seems to stay in place.
Another thing to consider is that the arm can act like a wrench on the ball when the kayak is moving. If the arm is hanging over the left side of the kayak, the resistance from moving through the water is going to push back on the arm and possibly loosen the ball. If it's on the right side, that same resistance is going to push back on the arm and tighten the ball.
I can't help with the navionics question. Maybe you can get someone with sidescan to see if they can find the wreck.