Upon updating to jenkins server 2.4 there was an issue with "FATAL: Jenkins has not been started, or was already shut down" being thrown when connecting to windows 7 VMs. The plugins that were also updated to the latest version were:

• Ant plugin
• Branch API plugin
• Docker build step plugin
• Folders plugin
• Github branch source plugin
• Github plugin
• Pipeline: REST API plugin
• Pipeline: Stage View plugin
• SSH credentials plugin

pastebin of the stacktrace can be found here:
http://pastebin.com/yLED34m6

Rolling jenkins server back to version 2.3 removed this issue.

-Djenkins.model.Jenkins.disableExceptionOnNullInstance=true flag was successfully passed to the jenkins server via /etc/default/jenkins, but this did not resolve the issue