If I remove the Explode & Lightning effect and leave the server next time I go back on i still have all of the effects. Anyway to prevent this?

How are you removing it?

@mbax using /vanish effects

If you are getting that every time you join, then you have granted yourself the permission node for it. This is a sign that your permissions related to this plugin are completely messed up.

What is your current list of perms you grant yourself for VNP?

vanish.effects.bats | true | never | global | global | none | deletecontent_copy
vanish.effects.flames | true | never | global | global | none | deletecontent_copy
vanish.effects.smoke | true | never | global | global | none | deletecontent_copy
vanish.vanish.off | true | never | global | global | none | deletecontent_copy
vanish.vanish.on | true | never | global | global | none | deletecontent_copy