Since you have set remote site replication to auto replicate there is not control when replication happens.
Check the logs and see when it relicates and check whether it finished successfully.
(Monitors--->Logs--->Log type "System"-->Log content "Server Activity"-->Select advanced settings-->Event type "Replication events")
Because of auto replicate settings your policy is applied to those clients after the replication only..
You can upgrade the servers to latest version(RU5). It has lot of features(GUP) and you can remove Remote site.
Or you can try Internal liveupdate server.
You can bring all the pc's to main server and configure liveupdate policy to point local distribution center(LU hosted server in remote site)
https://www-secure.symantec.com/connect/articles/installation-and-configuration-lua
https://www-secure.symantec.com/connect/articles/configuring-distribution-center-lua