OK, after binning the prefs it didn't create these folders on the initial startup, however once I set up the tvtv.com subscription and restarted EyeTV it started again.
Can't reinstall the app since it's a drag'n'drop effort, no installer. I suspect this is related to the tvtv listings which in my case are for France. Does anyone else use tvtv.com for listings within EyeTV? Got this problem?