Issues running a CB 3.1 app in a subdir of main site

I'm developing a new "admin" section to an existing site... an old
site dating back to 2002. They want the admin site to run as a subdir
of the existing site, e.g. Problem is, some
stuff isn't working right.

Most notably right now is that none of the preHandler() methods are
running. I tested this because I setup a separate site -- and it works fine when run that way.

The old site is all 100% procedural code, and does not have any pre-
request handler code (even in separate files).

Is there something I can do to fix this, or do I need to insist that
we setup a separate site like I did for my test?