Third party apps not launching

I'm at my wit's end with this. I would like to preface this by saying I've searched through the forums for an resolution to this problem to no avail.
I am using both the current version of the iPhone and iTunes software. I get various error messages when I try to sync (e.g., "device error", "duplicate file", "unknown error", you name it). I have even gone through something as drastic as reinstalling my operating system to factory conditions and reinstalling iTunes and the same thing. Of course the guys at the genius bar don't have a satisfactory solution to this problem so I have been sent home with a replacement unit the three times I have gone to see them.
The various error messages on iTunes, while irritating, has not affected my ability to use my apps. Now, I tap on an icon to launch an app and it does nothing. Two seconds later, I'm back to my home screen. The only apps I'm able to use are the apps which came with the phone.
I'd like to know what's going on. What is the fix for this? What can I do to avoid something like this occurring again in the future?
Thanks in advance for any help you can provide.

It sounds like you have lost your "permissions" for your apps. A similar thing happened to me last year on my 3GS. The only thing that fixed it was restoring my phone from a backup before I had the problem. I hope you get it sorted.

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