Permissions Help (A single player causing issues)

Ok so here's my problem. I restarted my server, when i did i was overwhelmed with errors in my console. I figure out that BukkitContrib is outdated, and that some of my plugins have been updated with Spout, i download the updates, no more console errors.

When the server started back up i noticed a few players i had promoted to the Citizen group had been put back to the Guest group. I check my Permissions users.yml and they are still there but its saying Citizens. I delete their names, and ask them to relog. Now permissions won't add their names to the users.yml.

Any ideas suggestions? When i manually add them and pr -reload, nothing happens. When i type /pr playername promote, it says promotion failed.

Any help is appreciated, thanks.

Info: I'm using Permissions 3.1.6, Bukkit 1000.