I see what you mean. I think it must be some IIS 7 configuration but I'm not sure what.
On my local machine using IIS 7 it works 100% of the time and on demo.mojoportal.com the log shows that the PageNotFoundHttpModule did handle the 404 and yet somehow IIS is returning the default 404 page.
It was working fine before I migrated from Win 2003/IIS 6 to Win 2008 IIS 7, and yet it works fine on my local Win 7 /IIS 7 machine. So it seems it must be a configuration difference somewhere.
Best,
Joe