Just required some sleep and some thought to sort this out. Having problems updating to 5.4 with errors referring to file permissions I finally gave in and updated the WoW installation as root. This resolved the issues with updating WoW. It also gave me issues with running WoW as a normal user. Problem is obvious when presented in those terms: permissions. During the update the files were replaced as root with root permissions. Once I restored normal user permissions I resolved my new problem.
I understood you shouldn't really run Wine as root. Now I know why.