Hi again James.
So, just to keep you updated on your issue, I did a bit of digging around internally to see what can be done, and here's how we'll proceed here:
as soon as I have a second (today or tomorrow at the latest), I will create an Issue Tracker entry about your issue (and link it here), then, if you could post the code you use for your users to log in, we'll try to reproduce the referral behavior on our end and if we can reproduce, file this as a defect and start working on it.
Sorry if it took a little while, since it touches both Analytics and App Engine, I had to make sure about the proper place for this to be handled.
Is that okay with you? (in any case, expect another message on this thread within 24 hours, where I will let you know of the link to the issue I've created for you).
Cheers!