Hey Joakim,
Be advised that this forum isn't the best place to get specific-issue technical support. For that, stackoverflow is much better, and you should use it in future if you have such a question, since we monitor there as well, although there's also a much larger user-base. From reading your question, at any rate, I have the following recommendation:
The docs link found in that log points you to the right place.
Here's the location in that docs page which discusses adding you App Engine app to your Google Apps Control Panel, and there's a
link to the Google Apps doc which discusses this in more depth. This should make your Google Apps authentication aware of the appspot domain and allow authentication.
Let me know how that goes for you.