I'm not sure if this is the correct place to add this "question" or "bug report", but it might help someone else that receives this message.
When i try to register a table that is created within my MS SQL server (without arcgis) and the column GDB_GEOMATTR_DATA exists the tool "register with geodatabase" will fail with the error 999999.
With the help of MS SQL Profiler i found out that the column that already exists were GDB_GEOMATTR_DATA.
Preferably the geoprocessing tool would not try to add this column if it already exists, or at least inform the user what column that already exists?
Additional info for others that may be searching for this like I was.
The RegisterWithGeodatabase tool now throws out 'ERROR 160328: Cannot create a table with a duplicate column' if the GDB_GEOMATTR_DATA column exists in the table you are trying to register.
For a python script, I am using 'try...except arcpy.ExecuteError' to trap for this. If ERROR 160328 is presented, it deletes the GDB_GEOMATTR_DATA and reruns RegisterWithGeodatabase(). Registration will recreate that column, so do not be spooked if you see it show up again.
MS SQL 14