pkg-config is supplied from pkgsrc and looks there already.

gnome-config is invoked by pkg-config as a fallback.  So it's not the
real error.

pkg-config needs to be to told what to report; just pkg-config and
module doesn't do much useful.

I have pygtk-2.0 installed.

fnord gdt 11 /usr/home/gdt > pkg-config  --atleast-version=2.6.0 pygtk-2.0 --libs
fnord gdt 12 /usr/home/gdt > pkg-config pygtk-2.0 --libs
-Wl,-R/usr/pkg/lib -L/usr/pkg/lib -lgobject-2.0 -lglib-2.0 -lintl  

So it seems that --atleast-version is not working the way you expect.

The man page says that it returns with differenet exit status, and
doesn't print anything.

      --exists

       --atleast-version=VERSION

       --exact-version=VERSION

       --max-version=VERSION
              These  options  test  whether the package or list of packages on
              the command line are known to pkg-config, and optionally whether
              the  version  number  of a package meets certain contraints.  If
              all packages exist and meet the specified  version  constraints,
              pkg-config  exits  successfully.  Otherwise  it exits unsuccess-
              fully.

              Rather than using the version-test options, you can simply  give
              a version constraint after each package name, for example:
                $ pkg-config --exists 'glib-2.0 >= 1.3.4 libxml = 1.8.3'
              Remember to use --print-errors if you want error messages.