[Prof Yaffle]

Then it's logfile o'clock - I'd start to follow the trail through what mysql is writing to syslog and/or security logs (to see what activity it thinks it's being asked to perform) and a debug log in Kodi (to see what it thinks is going on, e.g. is advancedsettings.xml being read correctly, is it trying to connect to the mysql server).

It sounds like you've got the basics set up okay... which I'm sure you knew, given your history and experience here.