I found an unexpected behavior occuring when using Shift Tool in ArcMap while having Parallel Processing environment value set to other than default (blank). It happens when I work on fresh Landsat data straight from Earth Explorer, previously untouched by any processing. I have described it briefly in this GeoNet thread, and below as well:
This happens regardless of where do I set Environmental Values: tool's processing window or Menu->Geoprocessing->Environments.
While testing Shift Tool, I also gave Rotate tool a try - it acts similar, it doesn't work with Parallel Processing. I attached a prtscreen of input image for Rotate tool and an output of the tool (plus both together). You can see the black NoData area moved to a different place, but the actual data stayed there and was sliced at the top. I haven't tested other tools.
This problem was tested on ArcMap versions 10.4.5686 and fresh 10.5.0.6491 and different Landsat images. I think this is a bug that should be reported, please let me know what do you think.
Best regards,
Adam
Since you have the data and the workflow, it might be a good idea to forward these data and examples through customer support so it can be investigated.