I don't know a lot about IPhones since I don't have one but I do have an iPod and if having music not show up in iTunes that is either on your phone or on your computer is the problem I had that same problem and I found a solution.

I don't know if this will work for your problem but I uninstalled iTunes and replaced it with this. http://www.winamp.com/

It sees every music file on both my computer and iPod and lets me just drag and drop files both ways without a hint of any of the problems iTunes gave me.

As I said I am not sure it will work for you but it solved all my itunes and iPod related complaints.