I've been having problems syncing an itouch 3g (running ios 4.2.1)

I can sync music to the iso 4.2.1, but whenever i do the music library messes up. It comes slightly out of order and in the artist part of the ipod, some artist's song become missing. whenever i sync my itouch on linux, i have to connect it to itunes and click safely remove sync through itunes. Does anyone else have this problem? do you know if it can be fixed? I do not know how to submit this bug to libimobiledevice.

Oh and i'm running maverick 10.10, with the neweest libimobledevice 1.0.4.