If the email is not using the Unsubscribe footer in Admin > Email, or using a custom link with the {{system.unsubscribeLink}} token, Marketo will not register an Unsubscribe from it. Custom unsubscribe links built into emails or email templates that do not use the token will not result in an Unsubscribe activity and will not count as an Unsubscribe on the email performance report.
I have this same issue and I've tried to understand this.
We have this link in our footer:
http://mrktoa.blueshieldca.com/bsca_unsubscribe.html
Are you saying that we need to adjust this in our email admin area?