SERVER SAYING OLD WHEN UPDATING! HELP!

Recently I have been having problems with updating to a newer version of Minecraft on my vanilla server. Whenever I update and I look on my server list it says Old and "Server out of date!". Me and some staff have figured out that something is wrong with some people's player.dat files because I have used Bukkit in the past which makes me have to delete all of them. So I delete the players folder and playerdata and replace them with the same name. When into the new update, still says the same thing (Old and "Server out of date!"). I really don't know what to do anymore. I don't want to make a new world and I don't want to delete peoples inventory, but if I have to I will. Please post some suggestions in the comments... Thanks!