I can confirm the same problem with a 3GS running iOS 5.
Device mounts properly and displays in Nautilus and Rhythmbox. Transferring 
files to device does not appear to actually update the device database. This is 
apparently an upstream problem; libimobiledevice.org suggests that this is a 
known limitation of the library. See the following comment:
"14.10.2011: iOS 5 music sync has a lot of changes. Linux users who want to 
sponsor the required implementations feel free to donate."

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https://bugs.launchpad.net/bugs/882039

Title:
  iPhone 4S will not sync

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