In the process of georeferencing about a dozen Tiff rasters, approximately five failed to complete the process on a first attempt. I am using ArcGIS Destop 10.5.1 and the georeferencing tool. I first fit the raster to the display area of interest. Then I have been using the standard rotation and shift tools to position the raster so it is easier to pick out control points to make links. I then create 2-3 links using an Affine transformation. When I am satisfied with the results (sometimes deleting a link and picking another control point), I do an "Update Georeferencing". However, after this point for 5 of the 12 Tiffs, the raster moves off from the display and only the rotation position seems to have been saved.
I then end up having to repeat the same process and it usually works the 2nd time! I cannot figure out why this seemingly random error is occurring.
I think I figured out the issue. Because I do the manual rotate/shift before doing control points, at times the raster can be aligned well by creating only two control points. When I did this, I apparently used my default (1st order polynomial transformation) instead of choosing a zero order transformation. When you try to do a 1st order with less than 3 control points it does not give an error message, it just deletes all the control points and apparently the last shift move.