If the custom workspace option is chosen, and the custom workspace directory is chosen to be in the workspace directory, the WorkspaceCleanupThread (if enabled) will always delete this directory, believing it's not associated with any job.

To reproduce:

• Create a job with a platform-appropriate path to a custom workspace in the workspace directory, e.g. workspace\custom
• Run a build to populate the workspace.
• Invoke the WorkspaceCleanupThread.
• The workspace will be deleted. Fine logs will show something like:
  

  Feb 23, 2011 5:20:55 PM hudson.model.WorkspaceCleanupThread
  FINE: Directory d:\dev\hudsonBuilds\workspace\custom is not owned by any project
  

Workaround is to not create custom workspaces in the workspace directory.