Hi,
It's probably not the scratches. I have lots of scratches on the transducer I use with my towfish. I have pulled the transducer over mud, gravel and even rocks and got some nasty scars, but no effect on the image. The auto setting of depth can sometimes jump up and down because of many reasons. I have seen my unit lock on the thermocline, layers of algea and dense clouds of baitfish. The unit does it's best, but the reality down there can, sometimes, fool the smartest depth finding algorithm. A way out is to set depth range manually and read depth from the image (and hope you are smarter than the unit), not the figures.
Rickard