Has anyone been able to successfully use the georeferencer to adjust alignment 
on a geotiff that already has positioning data?
I've been trying to make some minor adjustments to some drone generated mosaics.
My experience is the georeferencer seems to correctly load the geotiff with CRS.
It displays the projected coordinates and records GCPs in those coordinates, 
but it appears to then try to transform as though they were pixel coordinates.
Eg. the Source and destination GCP's Y values might be 6,300,000 and 6,300,010  
but the dy reported is not 10, it is approximately -6,300,000
If I ignore the problem the georeferencer runs correctly, but puts the result 
completely in the wrong place as suggested by the dy value.
This is happening with source, control points and destination CRS all set the 
same.

Is there something I am doing wrong or is this just a bug?  Seems to work fine 
if I run the geotiff through and image editor to remove the initial 
georeferencing.

Michael Dufty

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