Thanks for the response, I did log a support ticket in the interim and I'm sure they will be investigating. Just thought I might get a quicker response here. I'm relatively certain it isn't the expected behaviour.
Some background on the issue:
We use the API to create a deal and associate 2 contacts. An deal automation workflow then simply triggers emails to be sent to the associated contacts.
The email template I'm using has a Rich Text module that has a smart rule activated: If contact is member of a list - show different content.
If I send this email on it's own to individual contacts the smart rule works, however when the email is sent via automation through the deal workflow, the smart rule always shows default content, regardless of list membership.