I was doing an iPhone Ad Hoc build for a client and we came up against this error. Client and I are using DropBox to send the Ad Hoc .app builds back and forth. Randomly we would see this error:
The application "myApp" was not installed on the ipod "device name" because its resources have been modified
Turns out that DropBox touches the files inside of the .app in some way. The fix is to zip or Archive your .app and then put it up on DropBox.