I used the updater to install VS and suddenly our goto command spit out a message that we needed to restart the server or add an admin to the sniper.txt. Now, I have created the sniper.txt and rebooted the server and it continued to persist. It cannot be a permission conflict because my research into this issue told me VS doesn't use permissions? PEBKAC?

VoxelSniper has a /goto command. Due to it being a sniper+ command, it will tell users they need to be a sniper along with whatever the other plugin does to handle it.

You should be able to open the pluginy.yml of sniper & remove the command, let me know it you get it working/have any issues!

So we(fellow admin) thoroughly looked and I am fairly sure the file you speak of doesn't exist in the folders that were installed. I think my counterpart even Unrar'd some things.

The plugin.yml will be in the root folder of the VoxelSniper.jar.

This is part of the feature set of VoxelSniper.
Don't like it? Deal with it and wait for it to change.
This is neither a bug nor should it be treated like that.