This also happened to me. I didn't notice untill this morning when I tried to 
access my music on my iPhone. It displays "Updating Library... this may take a 
few minutes" and just sits there.
I recall that the phone was syncing a few times while it was connected and 
while I was playing music from it with Rhythmbox. I never received any errors 
tho from Rhythmbox or Ubuntu.

Running a clean install of Ubuntu 10.04 32-bit and iPhone 3GS firmware
3.1.3

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Rhythmbox automatically synchs/breaks iPhone
https://bugs.launchpad.net/bugs/579166
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