Alternate working directory not being used for child folders
After changing to an alternate working directory for a view (View -> Properties... -> Working folder -> Alternate), child folders continue to use the old working directory.
This happens when a child folder or folders (any folder beneath the root) has an absolute path for a working directory instead of a path that is relative to the root folder. Right-click on the problematic folder and select Properties... Change the absolute path to the working directory to a path that is relative to the root folder.
Author: Levi Bowman