Hi Sancho,
A very good advise at first - use a test system before using any new features or settings on a production. I am pretty sure you know that well but remember to follow that rule in real life as well.
Next you have to understand that the system's behaviour depends on many configuration settings but not the only one checkbox. When you select or clear a checkbox value then the system may use another settings to act one way or another. So you have to review and understand a whole picture how your system works. And believe me it's really hard to suggest or even to tell something when we can't see that picture.
Anyway, here are some general suggestions to avoid such loops:
* Use VSM customer with no email address specified to register such automatic responses from messaging system. No customer notification will be sent then.
* Use different email address for GFI automatic reply if possible.
* Use VSM stored procedure to make an extra filter for outgoing messages (Ian's suggestion).
* Use VSM stored procedures to make an extra filter for inbound messages.
* Use IPK Workflow Rule conditions to detect such logged incidents and do not send a customer notifications.
By the way, I just noticed an interesting inbound Email Server setting "Ignore Mail Server Report Messages". This one might be useful as well. However I don't know the system's version when this setting have appeared - you may not have it in 9.1.3 yet.
A few words about IPK Workflow Rules checkboxes. Continue and Cancel are only important when you are using more than one Rule Mapping. Autorun is related only for automatic assignment actions. As I understand neither of these checkboxes are important in your case.