I just went through a hectic four days involving a redirect loop in WPMU.
The issue turned out to be these two lines in the template-loader.php file (6 &7):
if ( defined('WP_USE_THEMES') && WP_USE_THEMES )
I use child theming with Canvas as a basis. When the issue was going on, I loaded twenty twelve and it still produced the redirect error.
If anyone has any insight as to how what in a child theme may cause this issue, it would be greatly appreciated to know.
As always... thanks...