Until there is a fix for Five-Column Springboard and iTunes 9’s App Arrange (Dev said coming soon). I do a little iPhone App Foo.
In iTunes Uncheck :: Automatically Sync when this iPhone is connected
Download from Cydia :: SpringBack (Allows you to save icon placement on the springboard)
1.Backup Springboard using SpringBack ::BeforeyouiPhone in to Sync or make changes (Only when you plan to sync, just plugging it in to charge should have no affect).
2. Disable Five-Column Springboard in Settings on iPhone.
3. Plugin iPhone and Sync.
4. Unplug your iPhone from Computer, Enable Five-Column Springboard, and Restore Icon Placement using SpringBack.
Takes less then a minute, and does the trick until things are ironed out.