Actually I meant syncing new apps, music, etc. Each time I do this (which I now avoid) I find all my apps scattered all over my iPhone screen. The user made folders are gone. A real pain to fix if you have many apps.
So every time you sync, your folders disappear? That isn't normal. Can you give us your versions of iOS and iTunes, and any sync settings you might think are relevant? (Do you auto-sync new apps, do you manually manage everything, etc.)
That will happen I you are syncing on two different itunes machines. Otherwise, you may have a caching problem. Try unchecking then rechecking the apps sync. Google would be my next step.