oops mada typo:
'iTunes could not sync bookmarks to the iPad "name" because the bookmarks are in use bu the iPhone.'
'iTunes could not sync bookmarks to the iPad "name" because the bookmarks are in use bu the iPad.'
a few days later, the problem seems not so frequent after directly updating to iOS 4.3
I've just had the same problem with my iPhone 4. This worked for me:
On your iPhone/iPad, quit Safari. (Press and hold the On/Off/Sleep/Wake button until you see the application's red Quit button appear.)
Go to settings>Safari and scroll to the bottom.
Press all three buttons: Clear Cookies, Clear Cache, Clear History.
Then,for good measure, use your customary syncing procedure to replace the Bookmarks file with whatever Bookmarks you are syncing your device with.
I have the same problem, but it was after buying a new Mac and setting up syncs. The bookmarks from the iPad disappeared and were not syncing through MobileMe, although it is working on my iPhone 4, so I turned of the MM sync and tried iTunes. After trying just about everything suggested in this thread (hard boot, clearing caches etc, shutting off all multi-tasking, getting rid of the Mozilla app, and so on) when I sync with iTunes I still get the message: "iTunes could not sync bookmarks to the iPad xxxx because the bookmarks are in use by the iPad."
How does one shut down whatever is using the bookmarks?