I had Xcode 4.1 preview 5 working fine but decided to upgrade to the final xcode 4.1 thru the App store. I uninstalled Xcode first...
sudo /Developer/Library/u
Apparently even after downloading and "installing" XCode from the Appstore and despite the long process after downloading where it appears to install it and the words "Installed" eventually become displayed next to it in the store. You must still manually install it again within your applications folder before it will work.
Odd.