Recently I discovered my ~/.fedora.crt was expired. I got a new one from https://admin.fedoraproject.org/accounts/gen-cert.cgi and dropped it in place, reran /usr/bin/fedora-packager-setup.sh and the resulting pkcs12 file was from the old cert! It turns out the cert gets copied to ~/.koji, so changing ~/.fedora.crt and rerunning the script doesn't work (without manually removing the copy in ~/.koji)
We've fixed this problem.