EngineYard Server rebuild is removing plugins installed into Jenkins

Each time I rebuild (via the EY Cloud panel) my CI master, the Git and GitHub Jenkins plugins are removed. Additionally, the version of the green balls plugin and rake plugin seem to be reverted to the default installed version and not the upgraded version that I have installed. All of my other plugins seem ok, except for these plugins.

Once the plugins are removed by the rebuild, an error is displayed on the Manage Jenkins page about unreadable config data present -- "You have data stored in an older format and/or unreadable data." This config data appears to be the GitHub plugin configuration being persisted in the config files, but as the plugin is no longer installed, Jenkins can't interpret it.

Why would the EngineYard Chef scripts remove these plugins?