Kixstart not setting values in registry

When setting values in the current user shell and user shell folders in a Windows 95/98 enviroment in a logon script the OS is completly ignoring. Should you the run the script from the desktop the values get modified. Windows 2000 pc’s on the domain have no problem with logon script values. I have used an account with a completly cut down config.pol file and Group policy object with the same result.