I recently upgraded to mu 1.2.5a from 1.2.4 and now I have a problem that may be a bug. My overall site admin account works fine, but all other users cannot login from "/sites/wp-login.php". They can only login from "/sites/username/wp-login.php".
If they try to login from "/sites/wp-login.php" they get redirected to "/sites/wp-admin/profile.php" and the page fires a "You do not have sufficient permissions to access this page" warning.
I run ubuntu feisty, php5.x, apache2.x, and mysql5.x and I've never had this problem before upgrading to mu 1.2.5a. I'm not completely sure that the upgrade caused the error, because I run mu for a small school and no one complained until today, but it definitely worked fine for me at 1.2.4 and I really haven't done anything of note recently other than upgrading to 1.2.5a. My mu uses subdirectories rather than subdomains.
This issue is mentioned in the forums, but there doesn't seem to be an available fix.