When I connect to my server I am automatically vanished, I don't know how to fix this also I cannot disable the lightning, fire or explosions which is extremely annoying :/

I've tried different permissions nodes and everything but nothing works!

If you're joining vanished then you've given yourself the permission nodes for that. If you're getting lightning, explosions and smoke on vanishing, then you've given yourself the permission nodes for those effects. Read the permission node documentation for this plugin (http://vanishnopacket.github.com/permissions/) and only assign the nodes you want.

I haven't given my self any permission nodes..before closing an issue make sure its resolved ? ...and this issue, is not