The new POIs that you added (those that are not visible), are they added to a new or an old category?
_EditLocation specifies which POIs a user/role may edit.
_EditLocationCategory specifies which categories a user/role may edit.
_ReadLocationCategory specifies which categories a user/role may read/list.
This must be setup both in SiteAdmin and VehicleTracker.
See the following topic for detailed explanations of the POI privileges: http://forum.gpsgate.com/topic.asp?TOPIC_ID=12572
Also, since you just upgraded, make sure that you clear web browser cache and reload the VehicleTracker page (Ctrl+F5) to load the new files.