The description of this logon setting in GPO reads as below.
..."If this setting is disabled and Synchronization Manager is configured for logon synchronization, the system performs only a quick synchronization. Quick synchronization ensures that files are complete but does not ensure that they are current."......
So I guess it might be doing a quick sync in your case. check sync manager settings..you can open it using mobsync from Run. and then click on Setup... If this helps then you need to figure out how to configure this for all users in the domain..
Offline Files