Does the output from the PerlApp command show inclusion of the File::Basename module? Some dependencies are not found correctly by PerlApp, what commandline options are you using? Have you tried telling it explicitly to include File::Basename?

side note: The PDK 4.0 version is much improved over 3.0. You have to uninstall 3.0 before you install 4.0 or it won't updgrade correctly.