"I simply delete the Apps and then I am allowed to install the updated App. This works for now."
Yes, you are absolutely right, this does work. I have posted recommending this in the past. But having said that, it should be qualified with the fact that it is essential to remove all vestiges of the unwanted application. Too often, cloned systems and copies prevent reinstalling an app.
You mentioned cloning as a potential problem. I use Super Duper to clone my drives for back up and occasionally use the clones if I have a problem with the main drive. This may be the source of my problems. I am installing OS X 10.8 and will make sure I am not using a clone to see if this fixes my problems. Thanks this info has been helpful.