I hate this problem! There seems to be a simple solution that SOMETIMES works:
Possible solution
Go to Build Phases -> Link Binary With Liibraries.
If you are having a problem with say Foundation.framework. Simply delete that one --- i.e., use the minus ("-") button at the bottom of the list.
And then add it again, using the plus button.
Clean the build folder. (To do so hold down ALT, then click Product -> Clean. You will see "Clean" changes to "Clean Build Folder")
Another possible solution
Be sure to read Matthew's answer here ...
iOS SDK broken ever after reinstall UIKit and Foundation frameworks not found
Look at the value of your "Framework Search Paths".
Another possible solution
Completely and totally uninstall XCode 4.3, use "CleanMyMac" to do so (it will try to find every associated component of the app you are trying to delete).
Then just use the App Store to (re) install XCode. As David mentions, this can sometimes fix this damn problem.
Why does it happen?...
I believe this problem can possibly happen in situations where you have, say, replaced your hard drive (i.e., probably using Carbon Copy Cloner or the like) or in some way the main volume on your Mac gets renamed or changed in some way. I think there might be a slight bug in the new "application-style" Xcode where it sometimes does and sometimes does not understand that sort of change in the paths.
I hope it helps someone!
It is an infuriating problem. I just had it happen again, in this case, because I subsequently deleted a copy of the "old-style" XCode from a machine. (It's perhaps better to utterly delete old-style XCodes (/Developer directory, etc) before installing the new-style XCode.)
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