I just created a new throwaway site to confirm this. It seems you can't download your previously deployed apps, but only applications uploaded by v1.4.0.

This is not true (meaning, it worked for me). Are you sure you used a command something like this?

  $ appcfg.py download_app -A <app_id> <some_folder>

If it doesn't ask for credentials, you should probably add the --no_cookies flag.

Yes, I did just as you suggested. Strange. Still no go.