I've got this problem as well, but it wouldn't fully complete a backup - as at the point it tried to transfer the purchase of "super monkey ball" (purchased directly from the phone) - the transfer would hang, thus forcing me to cancel the transfer (and presumably the whole backup) - hence I am in "backup hell" untill this is sorted.
The only way I can see around this is to ditch SMB; then re-purchase through the computer (once iTunes staff refund me of course)!
Anyone else experiencing this for iPhone purchased apps?
My backup went through the same thing. I had bought Super Monkey Ball and it transferred it to my iMac. If you buy an App you can re-download it at anytime without any extra charge.