Tracks listed under "Manually Added Songs" continue to re-appear When syncing music to an iPhone, iTunes give you the option to drag individual tracks to a section labeled "Manually Added Songs" to add them to the device (as opposed to adding all tracks of an artist, genre or album). The "Manually Added Songs" section not only contains tracks "cherry-picked" in iTunes itself, but it will also contain tracks the were added within the device itself after your last sync (for example, by using the iOS version of iTunes to re-download a prior purchase). 

This feature is behaving strangely for me: Tracks I downloaded manually from within the device a long time ago, continue to appear in "Manually Added Songs", even after I have manually deleted them from the device and even after I manually deleted them from the "Manually Added Songs" list itself (to avoid those songs being re-sent to the device on the next sync). 

Essentially, this odd set of tracks (a few songs from album A, a few songs from album B, etc) continues to magically re-appear on the "Manually Added Songs" list regardless of what I do. The only way to not get these tracks sent to my device is to manually clear the "Manually Added Songs" list every time before I sync my device. This is clearly not the way this feature is supposed to work--sync should "trump" what's on the device, so once the "Manually Added Songs" list is cleared, that should clear those songs for good. 

After complete re-installs of iTunes, iOS, OS X (for reasons not having to do with this problem), this problem persists even across two different phones. The one constant element is that we are dealing with the same iTunes (XML) library file. I would like to keep this file because of the play stats and whatnot, so if anybody can point me in the right direction (including hacking the iTunes library file), I would be ever grateful... I am tired of listening to those same songs! :P
When you delete songs on an iPod (or other iOS device), they get copied back the next time you sync with iTunes. This makes no sense, of course, but that's the way it works. (It correctly does not re-sync apps you delete, most of the time.) The only way around it is to un-sync the tracks - make sure they are not selected in the Music tab, or are not in any playlists, or uncheck the tracks and choose the Only sync checked songs and videos options. Or you can manually sync music to the iOS device, but that may not be what you want.