Cant say too much about what packages Ive got on my phone but for sure Ive got loads of flac tunes on my phone and non have doubled up names..!. I do have ogg but as for the support files Im not sure. Ive never had to update ogg that I know of but all of my tracks are just on the root and not in music as well does it really matter that the music is on the root? they all still show up in music. Can not understand why you have this issue..

Loz.