All the staff have "vanish.see" but when anyone goes into vanish, we can't see them, and when they unvanish, we can't see them either. Unless we leave the players area and reenter. This is affecting our Moderator's ability to do their jobs. Any help would be greatly appreciated. :)

Check with the vanish.standard permission.

That's just a small piece of it. :(

How would I get the full log?

In the logs folder?

Full startup log please :)

There you go http://pastebin.com/8AXD2FuJ

Sorry for the late reply, it was the holidays and I didn't have much time on my hands. http://pastebin.com/6zG1XTNz

Big request: Would you be able to test out your exact server configuration (PermissionsEx perms is really all I need) on a 1.7.10 CraftBukkit server and see if you experience the same issue? I've seen a ton of reports of Spigot bugs lately. I suspect this is one of them.

Whoops, I hit the wrong button, but I tested it, and I didn't have the same issue.

If you didn't have the same issue, it's a problem with Spigot. I've received a large number of complaints about visibility with the Spigot builds.