You should do after you charge up the batteries is to CHECK EVERY BATTERY CONNECTION. Make sure every battery cable is correctly wired. Then check that all the battery cables are tight against the battery terminals and are not rusted or corroded. Bad connections will cause any battery charger to not function properly.

After you've charged up your batteries and checked every connection and you are still having issues, it's probably safe to say you've got a golf cart battery charger problem and may need to service it or buy a new one.  You can purchase a new one: New Golf Cart Chargers.