Using ArcGIS 10.3.1
Reading the Desktop Help states that when setting current workspace in environment settings this is used when running tools (i.e clip tool). In ArcMap I used a base name in the input for the clip tool and the output is autogenerated, in theory it should use the current workspace which is: D:\ArcGIS Workspace\Default.gdb but it uses the path: Toolboxes\My Toolboxes\Default.gdb\Building_Clip1 which seems to defy the rules.
I have already set ArcGIS home to D:\ArcGIS Workspace.
If I set both the current and scratch workspace in environments the output defaults to the scratch workspace path.
I never trust default or globally set environment settings.
Every tool in ArcToolbox has an Environments button on the bottom right. I select it and check .... and some instances respecify ... the settings there. It takes less than 2 seconds, but at least you have confirmed your last line of defence against the results-go-where syndrome
- If the scratch workspace environment is set, the autogenerated output path will be the scratch workspace.
- If the scratch workspace environment is not set, the current workspace environment is examined. If current workspace is set, the autogenerated output will be the current workspace.
Try deleting the Scratch Workspace path, and keep only the current workspace path in Environment Settings.