Which version of MMA and MMW, how did you sync (USB vs wifi) and where did you modify the Playlists?

Are you sure you don't have that many files selected to be synced in the Device Profile (easier to check in MMW) or that your delete option is not set to remove the files (also in Device Profile)?

I sync my music and playlists.

Then i modified some playlist so i sync again and it seems to add "on top of the other songs"

IE: i have a 680 songs playlist. But when i synced it 3X its up to 2040 songs. Everytime i sync it just keeps adding up but only in the playlists.