Dependent Plugin Classes aren't properly loaded

We first noticed this problem with the Notifications plugin for ScriptRunner for Confluence, but it seems to affect any Scripted Plugin on Jira, Confluence, Bitbucket, or Bamboo.

Steps to reproduce with ScriptRunner for Confluence:
With the Notifications plugin installed,

• click on the Space Tools button 
• Click on the Advanced space functionality. 

You will observe that there are no Notification Built-in scripts visible. 

• Click on the Administration icon
• Click on the Script Runner Built in scripts option. 

Also observe that theres no Notification built in scripts visible.