Under /private/var/stash I have
Applications
Applications.8DAM3s
include
include,OjllZgG
libexec
libexec.6wZOza

and so on for the rest of the directories.

What is really weird is the currently used directories are the ones with the extensions. For example, the Themes directory is the old version before the 4.1 JB while Themes.Y25cw4 is the current Themes directory.

I did use PkgBackup after the limeRa1n JB so could that be the reason for the double directories and how can I fix this?

Thanks.