I am going to have to blow away my entire collection of songs, and let iTunes rebuild as if I just added them all. Again. This is the second time I have done this with the iPhone, and it makes five since I had an iShuffle about two years ago (and did it again when I added my iPod Nano 3G). It doesn't blow away my apps, photos, or other settings: just the music playlists.
I hate iTunes. I really cannot stand it. It takes 128-256mb of RAM, and slows my dual-core box to a crawl. In fact, the only reason boot into Windows now is because of my iPhone. I use Ubuntu almost all the time now, and if I could get VirtualBox to work with my iPhone, I'd only use Windows in a virtual sense. My boot time is abysmal in Windows.
Power on to GRUB: 10 seconds
Ubuntu: GRUB to Login: 25 seconds
Ubuntu: Login to usable desktop: 35 seconds
Ubuntu TOTAL: 60-62 seconds
Windows: GRUB to Login: 20-25 seconds
Windows: Login to usable desktop: 300-410 seconds
Window TOTAL: 4-7 minutes (depends on AV updates)
Most of the boot time is taken up by iTunes, Steam, various Java systray nonsense, and my AVG software, which sucked when they went to 8.0. It takes an average of 30 seconds to launch an application for the first time, like Firefox or the iTunes browser. I have tried defragging, but it doesn't help. Once Windows has been running for about 10 minutes, it's fairly snappy, but not when the iTunes browser is running. I have 3gb RAM on that box, and I never go above 50%, and still the Windows swap files is running like mad. Generally, the iTunes browser takes up 25-40% of the CPU at idle, and spikes up to 90% when I play music, and boy does it feel like it. My whole box groans and shudders like an old wooden ship in a heavy storm.
I installed iTunes on some VirtualBox VMs, and watched the memory and processor spike the same way. It needs at least a GB of RAM to run in a VM. Unbelievable.
Also, while you can get iTunes to play OGG files, the iPhone (or iPod/shuffle) does not. This is very irritating.