Jeff,
If they aren't biting a sting silver or other metal jig with a dropper fly, they aren't going to bite.
A lot of the marks I see deep this time of year I have to guess are bait because I can't get them to bite. Also, earlier in the season, I was noticing consistent marks over in the Honga near the bottom. It turned out to be grass that was starting to die off and drift out to sea. If you're fishing close to a river mouth, especially on an outgoing, this is a good bet.
To determine if it's vegetation, I sometimes drag like a 12" length of a 4" diameter alum pipe capped at one end by a chain behind the boat. The pipe goes along the bottom and scrapes up a sample of whats down there. It also lets you know if the bottom is muddy, sandy, or rocky.