ok, I figured this out, at least for me.
I have had this problem for a couple months, and spent multiple sessions with apple trying to fix. It went to level 2 support, then further, with lots of things we tried, but no resolution.
I have all my media etc on a NAS, and everyone (including apple) thought it was that. Apple also thought it might be quicktime, and a few other things. We uninstalled/reinstalled several times, remapped the nas drive to a local drive, physically moved the media from the nas to a local drive, none of these things worked.
What DID work was this:
go to APPS in iTunes, select ALL OF YOUR APPS. Right click on them and delete. ALL OF THEM. Note that it doesn't seems to matter if you say to delete the underlying files or not (after you say delete, it gives you a choice to delete the actual file like in iTunes when you delete a song- I tried it both ways, didn't matter).
Once this is done, sync your device.
Note that NONE of your purchases are gone, just the pointers to the files in the media folder (and the physical files themselves if you selected yes when asked). WARNING: You cant just delete them directly from the media/mobile applications folder (I tried that). You HAVE to delete them in iTunes; only there will it delete the pointer that is giving you the problem.
If you want to get all your apps back on your computer (which you don't need to do since they are still on your iphone/ipad device, but you may want to anyway) you have two choices;
1 just wait for them to update, and a new version will be downloaded then. this might take months for all the apps, but again it doesn't really matter since you don't need them locally; or
2 go to iTunes, Apps store, apps. Down at the bottom there will be 'purchased' which you will select, and it will load icons for each app you have downloaded. Now you can either download them one at a time, or select 'download all' and wait. I have over 400 apps, so it takes an hour or so to download them all.
I have now done this technique twice, and it worked both times. So I hope this helps you as well.
Let us know either way if you try this. if this is the solution for everyone, we are done, and don't need apple to do anything further, since it is non destructive.