The only reason I can think of that you would see differences between CRXDE Lite and Content Explorer was if you were logged into them as different users. Are you sure you are logged in as the same user?
The only other possibility is some sort error occurring when you browse in CRXDE Lite. Have you tried entering the path to your component in the search bar below the Save All all button in CRXDE Lite. It would be interesting to see if that generated an error message. You might also try tailing error.log which you try to navigate to the component, as well as checking your browser's JavaScript error console for any clues.