Too me a bit to figure it out but it looks like this branch is the culprit.
I was not able to set unique block configurations for my default AND administration themes. As soon as I upgraded to 6.x-2.0-alpha5 the problem went away. Is there any reason not to just go ahead with the 2x branch? It seems to be working nicely so far ... and most importantly it doesn't break my blocks page.

Anyone else get this?