Working with ESRI we found that turning off background processing and using the foreground method it worked fine. There is a 64 bit geoprocessing sp1 available but I have not installed it yet.
Turned off background processing and using the foreground method.
In ArcCatalog go to Geoprocessing at the top and select Geoprocessing Options.
In Geoprocessing Options Offcheck the Checkbox labeled "Enable" within the Background Geoprocessing section. (This is in the upper middle section of the GUI Window.)
I apologize for the inconvenience caused by this issue. I believe this issue has been addressed in ArcGIS 10.6 and later version. Which version are you using when encountering this issue?
If you are using 10.6 or later version and still see this behavior, I would appreciate it if you could detail the steps used so that I can follow it to reproduce the issue in house.