I have a similar problem. While uploading music to an iPhone 3G the new files are uploaded which can be seen in rhythmbox or any other music player, but not by the iPhone-music-player itself. Already present files also disappear from the iPhone-music-player.
This behaviour can be reproduced on iOS 3.x and iOS 4.x on my iPhone 3G.
I have a similar problem. While uploading music to an iPhone 3G the new files are uploaded which can be seen in rhythmbox or any other music player, but not by the iPhone-music-player itself. Already present files also disappear from the iPhone- music-player.
This behaviour can be reproduced on iOS 3.x and iOS 4.x on my iPhone 3G.
This problem can also be reproduced by other people regarding to http:// ubuntuforums. org/showthread. php?p=10222246# post10222246
The interesting thing is, that using banshee the sync works.