SharePoint ItemUpdated fires twice

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 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.
          //This is triggered by events other than check-in action.
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