Well, I'll be damned ... I wasn't looking at it properly due to the email address being a group ...
Anyways, both in x86 and x64, I changed the replyto email, and when I reply, it is in fact using the sender in the reply to.
Just tried it in the latest CTP of 2008, and the same problem resides. So now more than ever I'm curious to as what is causing this.
Making SQL do what we want it to do.