Ok. Try this. SSH into your iPhone/iPod. Navigate to /System/Library/Audio. Inside the Audio file there should be a UISounds folder. Copy that folder onto your desktop. Go through the files and see if any of those were altered. These files are the stock sound files the iPhone/iPod uses. The files are in .caf format, so be sure to have something like QuickTime to be able to listen to the files. I would figure that by restoring the iPhone/iPod it would revert back to it's normal state, but whenever you backup the device it leaves a "fingerprint" of what was on it and by restoring from the backup it will still have that "fingerprint". That's the way AptBackup works. If you find that one (or more) files have been changed you can download the originals from here.
Apple Forums & iPhone Forums, Mods, Hacks, News, Themes, Downloads, and more! | ModMyi.com - Downloads - Stock System Sounds
Once you have the files, just replace the bad ones with the new ones and see if it works. If it doesn't, I'll think of something else.
Cheers!!!