Google Apps "Aliases" vs. "Active" Domains & Linking to GAE

[Ryan Galloway]

I have a single Google Apps account and have several other domains, which I have either aliased to my primary domain, or added as an additional domain on the same account (for reasons of managing groups and users separately without having to maintain separate Google Apps accounts, which is nice), so on the domains setting page I have, e.g.

    mysite.com     Primary domain
    foo.com        Active
    bar.com        Domain alias for mysite.com

It seems like I can link "aliased" domains to my GAE app (despite others having issues apparently: http://code.google.com/p/googleappengine/issues/detail?id=638), but not the "active" additional domains.

They're either not listed in the available domains on the app settings page, or I get one of these errors:

"We are unable to process your request at this time. Please try again later. (Error #1000)"

"Sorry, you've reached a login page for a domain that isn't using Google Apps. Please check the web address and try again"

I have clearly established ownership over these domains via Google Apps. Why does linking work with aliased domains and not active domains? Is this a known issue? Is there a workaround or a fix besides creating a separate Google Apps account for the domains I want to link to my GAE app?