I think you’ve been hit by this “feature” of WordPress, others were caught out by it too.
There’s a very easy fix:

  • Edit your options database table and fix the siteurl value.
  • Now, open up wp-inst/wp-login.php and comment out the following lines: if ( dirname('http://' . $_SERVER['HTTP_HOST'] . $_SERVER['PHP_SELF']) != get_settings('siteurl') )
    update_option('siteurl', dirname('http://' . $_SERVER['HTTP_HOST'] . $_SERVER['PHP_SELF']) );

The next release of WPMU will have those two lines commented out by default.