Hello MP7,
You can try building mesh from the depth maps (Arbitrary mode) and then DEM from mesh (skipping dense cloud generation step), but without seeing the data I can't say, if the result will be much better.
If you can share the part of original dataset related to the problematic area, please send the download link to support@agisoft.com, so that we could perform test using different approaches and see, if the problem can be fixed in general case.