In my testing, I've had PermissionsEX work on default settings, I've also tried installing other permissions plugins as well as I've tried recreating the issue you are getting.

I can only conclude that with the all the information (even the extended info I asked for), you have a plugin conflicting with G2E-Vault or your permissions system is not configured correctly making the errors you claim to have likely an issue with that plugin.

If you find out it's a conflicting plugin, please let me know which one so I can work on getting my end compatible or so I can contact the developer of the conflicting plugin(s) to see if they can help me out.

If you still believe this is a G2E-Vault issue then please help me by proving so, as I can't prove it is myself in the 24+ hours I've been trying to help you.

I really don't like writing these types of messages because I prefer it's my fault so I can fix the issue, but sadly, I can't prove it's my fault and in testing on multiple platforms this plugin works fine with all permissions plugins as well as most economies that Vault and Register support (MultiCurrency is the exception).