Georeferencer output placed in wrong location

Question

I am using the georeferencer to align multiple Rasters. Out of 10 attempts 4 worked well, and the other 6 seem to complete, but it places the raster in the middle of the ocean (always in the same place).

Steps:

1. select the target (correctly aligned) raster
2. open georeferencer
3. open the mis-aligned raster
4. mark points on the mis-aligned raster using "from map canvas" and select same point on the target raster
5. go into options and set the CRS to the same CRS as the target raster.
6. run the georeferencer

Completes fine, layer is loaded, but not showing on map. When "zoom to layer" on the new layer, it places it out in the middle of the ocean - always the same extents.

All layers and rasters loaded are in the same CRS. Under settings/options/crs I have it to set new layers to the correct/same CRS. The target and loaded (to be aligned) rasters are all the same CRS and located adjacent to each other.

Here is the metadata from one that worked correctly:

Driver
GDAL provider
GTiff
GeoTIFF
Dataset Description
D:/Atlas/2017/Solana/Q1_2017/orthos/final/d2_flt2_aligned.tif
AREA_OR_POINT=Area
Band 1
STATISTICS_MAXIMUM=8184
STATISTICS_MEAN=6417.1849122364
STATISTICS_MINIMUM=0
STATISTICS_STDDEV=2864.6464188394
Band 2
STATISTICS_MAXIMUM=255
STATISTICS_MEAN=212.74360670194
STATISTICS_MINIMUM=0
STATISTICS_STDDEV=94.814437278534
Dimensions
X: 1323 Y: 5068 Bands: 2
Origin
315336,3.64444e+06
Pixel Size
0.244643,-0.244643
No Data Value
*NoDataValue not set* 
Data Type
UInt16 - Sixteen bit unsigned integer 
Pyramid overviews
Layer Spatial Reference System
+proj=utm +zone=12 +datum=WGS84 +units=m +no_defs
Layer Extent (layer original source projection)
315336.0186480708653107,3643195.5188297014683485 : 315659.6811249362654053,3644435.3687410801649094
Band
Band 1
Band No
1
No Stats
No stats collected yet
Band
Band 2
Band No
2
No Stats
No stats collected yet 

Here is the metadat from one that was placed in the ocean:

Driver
GDAL provider
GTiff
GeoTIFF
Dataset Description
D:/************a_aligned.tif
AREA_OR_POINT=Area
Band 1
STATISTICS_MAXIMUM=8508
STATISTICS_MEAN=1457.6642209972
STATISTICS_MINIMUM=0
STATISTICS_STDDEV=2982.9951333815
Band 2
STATISTICS_MAXIMUM=255
STATISTICS_MEAN=49.187032723175
STATISTICS_MINIMUM=0
STATISTICS_STDDEV=100.61475615584
Dimensions
X: 6540 Y: 6130 Bands: 2
Origin
-1.25767e+07,3.88515e+06
Pixel Size
0.282878,-0.282878
No Data Value
*NoDataValue not set* 
Data Type
UInt16 - Sixteen bit unsigned integer 
Pyramid overviews
Layer Spatial Reference System
+proj=utm +zone=12 +datum=WGS84 +units=m +no_defs
Layer Extent (layer original source projection)
-12576677.7759907748550177,3883415.9359119967557490 : -12574827.7554864250123501,3885149.9765376332215965
Band
Band 1
Band No
1
No Stats
No stats collected yet
Band
Band 2
Band No
2
No Stats
No stats collected yet