Incoming Email Case Capture- Autoreply loops

Has anyone figured out a way to manage the auto-reply loops that occur from the incoming case capture?  When we get an email we create a case and send a confirmation.  That confirmation sometimes gets tangled up in an auto reply by the customer where their auto-reply creates a new case and so forth until we have thousands of dummy cases.  I am adding in exchange filters as new wording for auto-replies come in but new terms keep arising.  I'm not sure if there is anyway for us to determine from the header if its an auto-reply or even why