I just went throught this same problem! I understand this is an old posting but maybe this will help someone... I can't be sure that I found an absolute solution for this but it just worked for me...
My father-in-law finally upgraded today from his iPhone 3G to an iPhone 4S. All he had on it was 26 pictures 3 sets of messages and his contacts and 1 app (he's old lol). I backed up his old phone and restored it to his new phone about 6 times all I could get was his pictures nothing else, not his messages or contacts. I updated his 3G to the latest ios as it was on 3.0 then I backed it up one last time(not sure if this made a difference or not). Then I went through these steps;
-erased all content on the 4S via settings>about>reset>erase all
-plugged into itunes and setup 4S as "ken's phone" using the newest backup which was from the newly updated 3G
-the update completed and the 4S was still in the setup screen where it asks simple questions to get your phone up and running
-I answered the normal questions until I got to 3 options; setup as new phone, restore from icloud backup, or restore from itunes backup
-I clicked restore to itunes backup
**keep in mind I JUST restored this phone from backup, but it was still asking me on his phone how to set it up**
-When I clicked restore to itunes backup it asked to connect to itunes, which I did. Heres the fun part...
In iTunes the phone showed up as "Ken's iPhone" which is what it should be setup as, it was not acting like it needed to be setup, although as I've stated on the iPhone it appeared that it had not been setup.
-Now I clicked back on the iPhone 4S and it took me back to the 3 setup options.
-I then clicked on "setup as new iPhone"
-I finished answering the rest of the setup questions
The phone turned on and had all of his pictures, messages, contacts, and apps on the phone! YAY!
I am not sure what made this work. I think it may have been because I updated the old iPhone 3G to the newest ios or maybe I figured out the perfect order to follow on the new un-cooperative phone. IDK! But I hope maybe this will help figure out this problem for anyone else who has it happen. Good Luck!