The Sysvol folder is just a repository for your policies. As long as it is replicating properly between DC's, it is just that, a repository. You might want to check the RSoP or gpresult on those machines to see what is actually applying to them.
As another option... If you have a group of machines that have a user policy that doesn't need to apply to anyone that logs in, you could put those machines in a sub-OU and use Group Policy loopback processing in merge mode to override the policy for anyone logging in.


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