When running the stand alone artex compiler certain registry keys need to be accessed, this require admin privileges the first time artex stand alone compiler is run. If you get the following error:
PM java.util.prefs.WindowsPreferences <init>
WARNING: Could not open/create prefs root node Software\JavaSoft\Prefs at root 0x80000002. Windows RegCreateKeyEx(...) returned error code 5.
Then run the stand alone compiler as an admin once to create the registry nodes and then it should be able to be run it as usual.