I have noticed that when I have op, I have all of the vanish permission nodes.
So when I join, I am in vanish by default. If I type /v to get out of vanish, bats, fire, explosions and lightning appear around me.

I have never had this issue in previous versions of the plugin.
Since the plugin has been updated to 1.6.2 this issue popped up.

Did you update your permissions plugin? I suspect that plugin is at fault, not VNP, or I'd have had an angry mob at my door when 1.6.2 came out.

Pex worked for all other plugins so I had not done this yet I believe. I will update it and see if it fixed the issue.

The issue has been resolved, thank you very much for pointing out pex might be outdated.

Glad it worked out! :)