Hi,
The difference in 2 different platforms is expected. Mostly, it's due to the logic/method each different platform uses and the way they track click-throughs.
For an ex: The email platform may track 1 click-through every time a link is being clicked, where-as, AA is complete;y dependent upon how you have implemented the 's.campaign' variable. In a scenario where, s.campaign variable is using the 'getvalonce' plug-in, only unique click-throughs would be recorded (determined per the expiration defined in the plug-in argument).
As a result of the above, the email platform would report more clicks for a particular code when compared with AA as the AA variable has been implemented to track only unique clicks.
The above is just a random example to help illustrate how numbers for 2 different platforms can differ.