Rob,
When you tested the Si transducer was this with or without the AS-Si-DB-Y cable connected?
Did it also do this while sitting still?
The problem still sounds like it is with the inside-the-hull transducer though. Usually the work better when there is water in the hull, so maybe a break in the cable and water getting in and shorting out something? I would replace the transducer and see if that helps. Just be sure and test the location before mixing any epoxy.