According to the screenshots there are a different number of markers in each project, and different numbers of projections for each marker.
In your workflow description you state that you added and marked the GCPs after alignment, so presumably you placed the GCPs manually on both occasions (which would already introduce scope for a difference between the two).
The marker with the greatest error by far in your 1.6.2 project is 2102, which now has 11 projections as opposed to only 6 in the original project.
Could it be that some of those 11 projections are misplaced? Or if you disregard this marker altogether do the errors improve?
Sorry i don't have anything more technical to offer, but often simple things can get overlooked!