Firstly my server setup as follows,
It's a FTB Ultimate 1.4.7 Server running mcpc+
What us causing the problem is I have a beta version of mytown installed (dose not have a perms bridge to allow group manager to work with it on its own)
Because of this pex is installed to give only mytown permissions as if I try to put permissions for anything else it does not work.
mytown is essential for the server since it protects against all the mods in ftb
since I have 2 permissions plugins installed vault is only picking one for snycing with and it picked the wrong one. I need it to use group manager to sync with as that has the perms so if you can get it to use a prefered plugin that would be great. If not any suggestions?

Is there any way to change the priority for pex and group manager? And its syncing to the enjin plugin for rank sync.

GroupManager will never get picked as a default permission plugin as it's a lower priority. Either ask mytown to recode and actually use Vault or give a selection for the permission plugin to allow you to specify which one you want, or don't use more than 1 permission plugin. This is not an issue with Vault as all permission plugins are registered and available to all plugins, the only difference here is which one is defaulted to plugins for use.

No Vault's priorities are simply a best-use assumption. Again, as I've already stated go ask the plugin developer to give the option to select which permission plugin to use.