Hi Patrick,
This does indeed seem odd. While Google Groups isn't the best place to raise a specific technical issue or defect report (although we can't know for sure until we investigate), I'll be happy to help by asking some basic questions here and hopefully we can either figure it out together or you can move on to creating a thread in the
public issue tracker, where defects are triaged, logged, and responded to with solutions.
So, the first idea which springs to mind is that somehow the new version is not the default version. You can check this in the
Developers Console in your project, under "Compute > App Engine > Versions".
The second thought which occurs to me is that since
Custom Domains have moved into being purely set-up through the Developers' Console and webmaster tools, something may have changed or need alteration on your side. Could you provide a screenshot of what you see in "Compute > App Engine > Settings > Custom domains"?
Finally, are you the user who initially verified the domain, owns the domain, or attached it to the App?
With this information, it'll be more clear what's happening for your custom domain mapping.
Best wishes,
Nick