I had the block region module installed, and now that I've uninstalled it, I can't control the visibility or assignment of blocks in my themes. I have to go into the database through phpmyadmin and change the values manually to cause the blocks to show up where I want them. Blocks that were created and assigned before the module was used are working properly. New blocks will show up on the default theme, even when they're only enabled for one of the other themes, and they don't show up in the theme they are enabled for.

duggoff