As taken from http://drupal.org/node/61247 :

Admins should be able to set up different block layouts per theme. I intend to do so for "portals" and allow easy navigation. Also, what I thought were individual theme layouts didn't work (as I said, see thread).

Comments

Crell’s picture

Crell commented
Version: x.y.z » 6.x-dev
Status: Active » Fixed

If you go to admin/build/block, you can separately configure blocks for each theme on the site.

Anonymous’s picture

(not verified) commented
Status: Fixed » Closed (fixed)