Hello Christina and Massimiliano,
We came across this thread while researching the same issue. We can confirm that the same thing is happening in our case. GCPs are not being taken into account even after multiple reoptimizations and numerous runs of steps 1, 2 and 3. It seems that the model simply does not include any corrections from the GCPs entered. This is even displayed in the ray cloud as the projected points remain in their original positions and elevation following GCP addition, reoptimization and step 2 densification.
We are using a Sony Camera and survey grade GPS so it is not an issue with a specific drone. Additionally, our GIS specialist set our datums which have been confirmed as correct for our EXIF location datum and GCP location datum.
The interesting part, though, is that we are seeing this with 4.0.25. You said that you downgraded to 4.0.25 and the issue went away. However, being that your original post was in November, and that 4.0.25 was the current version at the time (the new version came out just yesterday, December 14, 2017) I am wondering if you misspoke and that you were using 4.0.25 and downgraded to the previous version from that. Or, were you testing the next version and downgraded from that?
We have contacted support but have not received a response as of yet.
Thank you for your help,