And do you have multiple processes running on 3306?
Are you 100% sure the details you have in config.lua match up?
Can you paste this section of your config.lua, and obviously leave your username and password blank:
Lua:
-- MySQL
mysqlHost = "127.0.0.1"
mysqlUser = "root"
mysqlPass = ""
mysqlDatabase = "mydbname"
mysqlPort = 3306
mysqlSock = ""