Transferring apps from Iphone 3Gs to PC so i can upgrade

I have tried everything i can find to transfer my apps from my iphone 3GS to itunes on my PC so i can upgrade the phone but nothing works..Right click on phone on left side of screen, click transfer purchases and it only transfers 1 app which was a free app....I have synced the phone/ back up a couple times in the past couple weeks but it takes 4-6 hours to complete and still only shows 1 app in my itunes library...I dont have that much on the phone..150 apps....50-60 pictures and address book...does it always take this long ? Help.....Jay

Just FYI, when I did this, I had to manually select all the Apps to reinstall after restoring the iPhone4 with my iPhone 3GS backup. Most of the data for those apps transferred over with possibly one exception - a game (Nanosaur 2) in which my save games all disappeared.
I guess what I'm curious to know is, when you restore from a backup, shouldn't the Apps automatically restore and be in their previous positions? I had to go back and manually rearrange all my Apps which took quite a bit of time.

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