Apps disappear after syncing with itunes

I have a problem. it only started after i bought my new iMac and migrated all my docs etc from my macbook using Migrate Assistance. when i download apps on my iphone, after i sync with itunes they just dissapear.
HELP please

I know I am late in posting to this discussion but I had to put my two cents in. I am having the exact same problem on my 3GS. I use a PC to connect to itunes and more often than not after syncing is complete all of my apps have gone out of the organized folders! I wouldn't complain if I only had 20-30 apps to deal with but I have 495! I have called Apple on this problem several times and they have continued to plea ignorance saying that they have never had anyone call in with this problem before! Obviously this is not the case by all of the people writing about the same thing! I hope that Apple will get with their programmers and figure out what the heck is going on...we deserve better than this! Mr. Jobs would not be so well-off without us so he needs to take better care of his customers! Well, I FINALLY talked to someone that seemed to have a solution to my problem! I thought that you only needed to organize your apps into folders on the actual phone...nobody had asked me before if I had organized them directly on itunes. I am in the process of doing this now and I hoping beyond hope that by doing this my folders stay organized! Although, there was one time when I was just sitting at my desk and my folders all became disorganized when it wasn't even plugged into any computer or being charged with a wall outlet! We will have to wait and see!

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