How does the client know if the GPP item is applied? Match the UID of the FilterRunOnce setting in the XML file of the GPO on sysvol to the UID in the key below. Delete the one item in question and perform a gpupdate /force for the setting to reapply.
HKCU\Software\Microsoft\Group Policy\Client\RunOnce for user settings
HKLM\Software\Microsoft\Group Policy\Client\RunOnce for computer settings