Group Policy is refreshed every 90-120 minutes. Settings that can not be forced in these background refreshes are applied at logon. You should not have a problem with "some" settings being applied, especially after at least one reboot.
POSSIBLE ISSUES
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1. On machines that have a slow connection, then some policy settings are dropped intelligently. If you are on remote connections, VPN, dial up remotes, then you can force the computer to wait untill all policy settings have been applied, by changing the GP Settings in the GPO to apply Synchronously, and set the Logon options to "Always wait for network before loading windows". This is because one other issue with slow connections, is once a machine has been authenticated on the domain, a local cached profile is stored on the machine, that means that it enabled you to logon on with your domain account, even when you have a slow/or even NO connectivity with the DC, or any other network resource. Chaning the Wait for Network means that the users can not authenticate to their domain users desktop untill the network connection has been established, therefore forcing all policies to be applied, again, slow connections may drop some settings.
2. If you have a very large network, which contains a number of replication servers, and have alot of data transfer. You may be having replication issues, or just the replication is slow. Do you get the same kind of issue, having to wait a long time, after creating a new user on a DC, wait for a while for the AD to be updated on the all the replicated servers?
Hope this Helps.
Neil J Cotton
njc Information Systems
Systems Consultant