This question has been answered by BobRay. See the first response.
I don't know how notify404 works, but an alternative is the LogPageNotFound extra, which will create a log of the 404s and show you them in a grid (which you can clear periodically).
<base href=[[!++site_url]]" />
Be sure you have this code (with the exclamation point) in the head section of all templates (especially the one used by the log report page):
<base href="[[!++site_url]]"">
Worst case, you can clear the log just by deleting the file. IIRC, it's in core/logs/.
Sorry, that would be my fault (unless your default template is empty). I assumed it would get the default template.
Is your default template empty? If not, I'll try to put in a fix.