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I love Choo Choo as much as everyone else here, so Ive decided to drum up a quick solution for this whilst Apple hopefully fix it.
1. Lets re-download our favourite little tune here:
http://www.mediafire.com/?t65ze5gzu98tos7
2. Youll need iPhone Explorer to put it on the phone. No, you do not need a jailbroken phone to use this software. Just plug your iPhone into your PC via USB and done. Grab a free trial of that here:
http://www.macroplant.com/iphoneexplorer/
Alternatively, those with other iPhones can use iFile to do this all from the iPhone itself.
3. Navigate to System/Library/Audio/UISounds/
In iPhone Explorer click your iPhones name, then Root, then follow the path above.
4. Drag and drop the new (or old) Choo_Choo.caf file and replace that existing rubbish!
5. Reboot and thats it! Enjoy.
MacBook Pro 17-inch/2.8GHz/4GB RAM Mac OS X (10.6.7) iPhone 4, iOS 4.3.1