I don't see any corruption in the Debian package. The md5sums are correct compared against downloaded war files and the information contained within the .deb. Are you sure that you have the right version installed?

$ mkdir /tmp/jenkins
$ cd /tmp/jenkins
$ wget http://pkg.jenkins-ci.org/debian-stable/binary/jenkins_1.565.2_all.deb
$ mkdir jenkins_1.565.2_all
$ dpkg-deb -R jenkins_1.565.2_all.deb jenkins_1.565.2_all
$ wget http://mirrors.jenkins-ci.org/war-stable/latest/jenkins.war
$ wget -O jenkins-1.565.2.war http://mirrors.jenkins-ci.org/war-stable/1.565.2/jenkins.war

$ md5sum jenkins.war jenkins-1.565.2.war jenkins_1.565.2_all/usr/share/jenkins/jenkins.war
e53d793e42d1686ab103960dbd17979a  jenkins.war
e53d793e42d1686ab103960dbd17979a  jenkins-1.565.2.war
e53d793e42d1686ab103960dbd17979a  jenkins_1.565.2_all/usr/share/jenkins/jenkins.war
$ grep jenkins.war jenkins_1.565.2_all/DEBIAN/md5sums
e53d793e42d1686ab103960dbd17979a  usr/share/jenkins/jenkins.war
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