try reinstalling your iTunes. If not, I'd say restoring is the best option but you'll lose your jailbreak so i guess you have to live with it..
I've been having trouble transferring to my Iphone 4 (Jailbroken. 4.3.1). It takes 5/10 minutes for just one song to transfer (I reset it to "manually manage my music" mode recently). I am not facing any trouble when I'm copying apps. I haven't updated my Itunes in a few months and have not had this problem with my Ipod Touch 4th gen.

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