Itunes won't let me backup my apps!!!

[exaccord]

I have searched google extensively to no avail.

I recently got an iPhone4. I had a iPhone3Gs. I have a TON of apps on the 3gs that I would like to get off that phone and onto the new one. I was running an old firmware (3.1 something) I updated it in iTunes to the new 4.2.1. The 3gs has been jailbroken since the 3.1 update. And I obviously gave up the jailbreak with the new update. (I dont need it jailbroken anymore, I just need my apps!)

When I sync the 3gs my apps don't get added to iTunes. I tried right clicking on the phone and "transfer purchases" and it starts to transfer, but quits after trying the first app. I tried to download an app in the store, then sync again, nothing. I also tried to "verify computer" and still nothing.

I then tried to back up the phone to a disk and it only transfered some songs that I bought, no apps, and not even all my songs.

I thought about jail breaking the phone and using winscp to pull the apps, but I don't think winscp has that capability.

Can anybody please point me in the right direction to get this problem fixed (without going to the insanely crowded "genius" bar)

I am running windows 7 64 bit. Thanks

[dotFIVE]

Are these apps legally purchased or did you get the pirated version off of Install0us? If it's the latter, I'm afraid we won't be able to help you here.