When a process is performed windowed, the window doesn't load any XenForo scripts such as deferred. This keeps the process as smooth as possible since it's all Javascript driven.
However, when you load any other admin page, it should be running deferred tasks. If the deferred script is not loaded on regular VaultWiki admin pages, then this is a bug. However, if you can see that the deferred script is being loaded, but perhaps returns a 500 error, then there is an error inside the deferred task itself, and you might have to check Firebug or your logs to see what it is.