Hello d.portillo,
According to the screenshots here might be some considerable difference in alignment, therefore the depth maps are also different.
If we can re-use the images that you have already submitted to us, can you send the projects for both cases to support@agisoft.com, so that we could re-build the depth maps and reproduce the results? (to reduce the project size you can remove the depth maps, dense clouds and other processing products, but sparse cloud).
As for the depth maps display problem, which quality you are using and whether there are any photoview related tweaks enabled?