Is there any way to change the priority for pex and group manager? And its syncing to the enjin plugin for rank sync so I cant edit the plugin so you can give an option for a preferance as its not mine.

This is not a Vault issue. This is an issue with your other plugins choosing only the default returned Permission system to work with. There is no way to change what is returned back as the default in Vault, and this is not within Vault's scope. If you want to be able to configure what plugin is getting linked to you need to be asking your rank plugin or whatever other plugin isn't linking to the one you want, for the ability to do this. If you have a question on an already closed topic you can still respond on it.

Ultimately: Don't use 2 permission plugins, it's completely unnecessary.

Yes I know I shouldn't use 2 permissions plugins but the beta mytown demands pex to run and allow users to use mytown commands etc. But does not allow use of any other permissions on the pex config so I use group manager to do that. I will attempt to contact the cuurent dev of mytown but I doubt they will deal with this and I dont have the knowledge to change it myself. I have contacted the enjin team and they still have not replied. So I asked here , thanks for the answer though.