Make sure that you are not applying your settings in an Unattend that is set its Reseal setting to Audit. If so, all those customizations end up being applied to the Administrator account only! Once you sysprep, those settings "seem" to disappear, since the account you create and log in with doesn't have them. If you were to enable the Administrator account and log in with it, you will see those settings. So what needs to be done is those settings must only be applied during OOBE, or use registry keys to set those settings to the Default or All Users accounts.