All the code I used is in this thread on bukkit.
Vault, PermissionsEx, and CraftBukkit were on it's latest builds.

http://forums.bukkit.org/threads/vault-not-getting-groups-per-world.297617/

This appears to be an issue in your own code.

EDIT: Not quite sure what you're trying to report here the formatting on your code makes in not easily distinguishable on what you're actually trying to do.

The other reason I don't think it's Vault is because Vault doesn't contain any UUID methods, so you're clearly not using Vault methods where you reference 'vault.' Indicating that you're using a bunch of wrapper functions. I can't debug your own code that doesn't even link vault directly.

I get the UUID to my vault methods, but then I use bukkit and use getOfflinePlayer or whatever is need for you latest build.

Like this:

return this.permission.playerInGroup(world, Bukkit.getOfflinePlayer(uuid), group);

If that's what you're calling then PEX is not returning back a true status. Vault doesn't do any special translation for PEX and that call.

I looked at the source code, and the method you call is the same method that pex calls for to get the groups for /pex user , but there not returning the same values which is weird.