The ItemUpdated event does fire twice - by design. Once when the item is actually updated, and then again when SharePoint is done checking in the item.
See http://www.simple-talk.com/dotnet/.net-tools/managing-itemupdating-and-itemupdated-events-firing-twice-in-a-sharepoint-item-event-receiver/ for more info on that. 
Some people use a workaround like this:
if (properties.AfterProperties["vti_sourcecontrolcheckedoutby"] == null &&    
              properties.BeforeProperties["vti_sourcecontrolcheckedoutby"] != null)
{
           //This is when the update event is triggered by check-in.
}
else
{
          //This is triggered by events other than check-in action.
}