Carl,
Ok, so I assume you are setting the "Inbound Mail" as the on interaction status for a workgroup that is dedicated to email? If not, where are you setting it?
My guess is that the first issue issue is down to the email being transferred directly to Agent B and therefore no longer being associated with the Queueand therefore not picking up on the various automatic statuses.
I'm not sure why the second issue is ocurring - you might need to open a ticket on this.