Most likely you did multiple syncs in one session of emplode.
There's a bug that doubles the number of rows for the Favourite Visuals every time you sync, except the first time. If the file gets larger than 4096 bytes, only the last 4096 bytes will be read and interpreted, leading to missing stuff.
Work-around: close emplode and restart it after each sync.
Fix the current situation: IIRC it can be fixed if you in emplode go in and remove all Favourite Visuals for all sources - via the GUI, not by editing the config.ini manually - and then sync.
Close emplode and restart it, pick Edit config.ini - it should now be OK. Then you can select your Favourite Visuals again - via the GUI. Remember to restart emplode after each sync.
There's probably a FAQ on this issue... Ah yes,
here...
/Michael