User Preferences not applying until 2nd logon

We are experiencing a weird issue with new users logging onto our Windows 7 clients.

Some computers have had a number of settings applied to the default user profile and also some settings applied via User Group Policy Preferences.

When a new user is logged in the new .V2 profile creates and applies many of our Default User settings, however none of our Preferences have applied. A logoff and log back on is required to get the preferences to apply. This is frustrating because we would like to apply the setting "Apply once and do not reapply" and if these is selected the system believes the Preferences have applied (which they dont) and will not try again.

Has this been seen before?

Are there any policies that could be applied to force down User Group Policy settings at first logon?

Thanks