@Kevin Windrem Is there more information needed to diagnose the issue? This is 3.00.36 to .39 upgrade.
root@FlyingCloud:~# /data/GuiMods/setup
--- starting setup script v7.46
creating file set for v3.00~39
ERROR v3.00~39 dbus_systemcalc.py no replacement file
ERROR: incomplete file set for v3.00~39 - can't continue
Package Manager, SetupHelper, ShutdownMonitor, RpiDisplaySetup, RpiGpioSetup got upgraded with no apparent issues.