If you open an Xcode 4.x project at Xcode 5 and then open a xib at Interface Builder, you will get an alert:
I have tried the above solutions, but as other users pointed out, didn't seem to work well... Strangely, after downloading Cocktail for Mac, and cleaning up broken preference as well as caches and other junk (which I did just to maintain my aging Mac) the "Always Upgrade" mistake was finally fixed!!
I haven't bought cocktail, honestly, you can use it for free for ten launches or something. So, you can go ahead and get your Mac cleaned up and fix that burden along the way.