Similar toexcept that it's happening to me in the latest 6.x-3.0-beta3 release. This was working fine in beta2 for me (i.e., I could see the blocks page in my custom theme) but since upgrading to beta3, admin/build/block now displays in the Rubik theme.
I'm basically unable to assign blocks to sidebar regions, now. Any ideas?
Only other thing updated alongside Rubik with the Tao base theme.