Itunes doesn't sink apps

When going to update software on phone (3GS), I got a warning that the phone contained purchases that are not backed up. I made a manual backup of all files and data and then updated phone. As expected, the apps I had bought had gone from phone. I was able to reinstall as appstore remembered them, but had to sign-in to things again and all my games progress has been deleted (ah well). A friend has just posted on Facebook with the same problem- any idea what is going on? I have tried every option possible to back up apps on itunes. The apps tab on itunes shows all the phone screens but nothing in the left hand column, no matter what I do.