Just after Restore iTunes syncs everything (music, video, pics) the usual as well as the typical backup. I install some my stuff from Cydia, again the things I always do: MobilePatch thing from *********, SBSettings, Netatalk, Terminal, Finder, MobileCinema., I even do the install an app from iTunes first business before installing anything cracked.
I then sync with iTunes and it does the backup like it supposed to but will not sync Music, Movies, or apps any longer. No error nothing just no action.
In all the times I've jailbroken this has never happened...
Make sure you have everything checked that you want synced. Before you sync reset all your warnings. On the left hand side of iTunes, right click on your device and choose 'reset all warnings' just to see if you actually get any errors.