But in the new series, everyone knows that the timelords all died, even though, again, it all happened in the past. If that makes sense. *head explodes*
I would argue that only some do. The few times he's told people he's from Gallifrey they tend to get pretty scared.
Also, even if they know that they're all dead they haven't forgotten them. So theoretically the scanner should still have recognized him as the Doctor, maybe coming up with a "deceased". Afterall, it knew who Nefratiti was and by the time of this story she'd been dead for 2,000 years!
Any how, you're right. Doesn't make much sense. :lol