This change (to use -1 as the registry root) was made the default in AdminStudio 5 to reduce excessive auto-repairs of the shortcuts that were ocurring in AdminStudio 3.5 when the package was deployed per-user (the non-advertised shortcuts were causing auto-repair).
If you would like to override this behavior (you know your setup is for a single user only), you can set MultiUserShortcuts=N in options.ini to return the the previous behavior.