I have set up http://www.footballverdict.com and it's hosted on Google App Engine. Everything works fine. You can visit the custom domain without problems. For some reason when I do a search on Google for "football verdict", the results show startorsit.appspot.com/ask and startorsit.appspot.com/about. There is no footballverdict.com in sight for the main site! It's been at least two months since I hooked up the custom domain. The blog sub-domain does show up in the search results, but that's because it's not hosted on Google App Engine.
Does anyone know how to get the custom domain into the search results and remove the appspot.com sub-domain?
The easiest way to handle this is to have your app detect if it's being requested on appspot.com, and if it is, send a 301 to your canonical domain. Search engines will pick up on this and start listing your canonical site instead.
The answer? Canonical URLs.
Google Webmaster Tools has a great little blurb about it here, and Yoast has another one here.
I hope this gets you pointed in a good direction.
Best of Luck! ~Isaac
Are you using google webmaster? I think this might help. http://www.google.com/support/webmasters/bin/answer.py?answer=83106
It will still take some time for the updates to get into google tho(up to 180 days).