APT Black Magic
Be sure to actually check the listed paths in the Packages.gz file to
make sure that they are pointing to the deb files in question.
It sounds like you have the Packages file written in the proper format
so that it can be added to the package tree via APT or Synaptic
(frontend to apt), but that the locations listed in the Packages.gz file
I had a similiar problem with a previous version of Debian. You have to
take the tree structure of the standard repository into account when
making your own local package collections.
I hope that helps!