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The checksum as part of debian packaged jenkins is relevant because the checksum matches my installed war. So that means my war didn't corrupt after the fact. The checksum from the war is different than what is [provided as a direct download][1]. When I overwrite /usr/share/jenkins/jenkins.war with the [direct download war][1] and restart jenkins /etc/init.d/jenkins restart... our instance behaves normally once again.
I don't know the build/packaging process so it's entirely possible that the jenkins package is different in how it builds so the checksum will always be different than direct download jenkins. However, I opened this report because our instance of jenkins is broken when using the package version of jenkins.war and not broken when using the direct download version.
[1]: http://mirrors.jenkins-ci.org/war-stable/latest/jenkins.war