The problem is that the Packages.gz package contain only latest version.

wget 'http://pkg.jenkins-ci.org/debian/binary/Packages.gz' -O /var/tmp/Packages.gz
zcat /var/tmp/Packages.gz
Package: jenkins
Priority: extra
Section: devel
Installed-Size: 65795
Maintainer: Kohsuke Kawaguchi <k...@kohsuke.org>
Architecture: all
Version: 1.556
Replaces: hudson
Depends: daemon, adduser, psmisc, default-jre-headless | java-runtime-headless
Conflicts: hudson
Filename: binary/jenkins_1.556_all.deb
Size: 61229082
MD5sum: c3131e52fcd9e9157aab681f44800a4d
SHA1: d3544551374137432608d3e31d7cc68cab5f031b
SHA256: 73e220997aec0ed48982ba803f6fa0e60fa4143a837cb0111fac448f8b7b7cb0
SHA512: f3642cb26def332feeb63cfc12dd919625eba9778c66ba08f23f12c0de05abf704c949016ea65c204087b1e83dd3b49e1463544747b5a8b1230df90969bd32b0
Description: continuous integration system
 Jenkins is an application that monitors executions of repeated jobs,
 such as building a software project or jobs run by cron.
Homepage: https://jenkins-ci.org/

Most probably somewhere in the build shell script there is a command like

sudo dpkg-scanpackages . /dev/null | gzip -9 > Packages.gz

If that command is run incrementally, it should be >> Packages.gz. Or it should be run in the directory where all packages are located (can take some time). Let me know if I can help fixing it.

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