Im installing Jenkins with ansible so I have all plugins pinned to a version and then I install them with jenkins-cli. The plugins that are core to Jenkins won't upgrade this way (doing it from the gui or manually dropping them in the plugins folder works). I tested with cvs plugin, antisamy-markup-formatted plugin and Maven plugin

Tried both to upgrade plugin from url and download the file yields the same result (i.e Jenkins wont upgrade the plugin. Other plugins works fine, just those who are in the core won't work). This example is with the antisamy-markup-formatted plugin

_wget "http://updates.jenkins-ci.org/download/plugins/antisamy-markup-formatter/1.3/antisamy-markup-formatter.hpi"

java -jar /home/jenkins/work/war/WEB-INF/jenkins-cli.jar -s http://localhost:8080/jenkins install-plugin antisamy-markup-formatter.hpi
Installing a plugin from local file: antisamy-markup-formatter.hpi

service jenkins restart

grep "Plugin-Version" antisamy-markup-formatter/META-INF/MANIFEST.MF
Plugin-Version: 1.1_

No interesting output in the jenkins.log