I'm wondering if maybe the way you are updating your source tree might
  be causing source files to retain a last modified time equal to their
  last change time instead of equal to the update time.

This is with a fresh checkout and an empty /usr/obj.
So the timestamps are those of the last modification in the repository.

  As you may know,
  CVS, for example, ensures that files modified by "cvs update" have their
  last modified time set to the time "cvs update" modifies the local copy
  so that regardless of when the change was made any changed files can
  never appear to be older than the last local build time.

I'm aware of that make-coddling behavior :-), but this is with a fresh
checkout and hence last-checkin mtimes.  I am installing onto a fresh
1.6.1 install.  The problem is that the mod time of e.g. files in
/usr/include/net in the filesystem from the install is the date that
the release was made, not the date that the file was last modified.
Regardless of correctness issues, I actually like it that the files in
/usr/incldue have an mtime of their last actual change in the sources.