Lammert, thank you very much for your reply.
Now it gets interesting. The default Ubuntu install of mysql is Root > etc > mysql and that folder is still present. It doesn't have the actual DB server but it does have my.cnf
Because I removed mysql and them reinstalled in another location opt > lampp... the paths will be totally wrong. I did however install mysql client through the package manager so it will almost certainly be trying to use the default my.cnf file.
Should I un-install mysql client and do a manual install from source, or just edit the default my.cnf file.