WPMU is adding some extra information to the end of wordpress’ username cookie content.
For example, the old cookie content is simply “admin,” while the new cookie is “admin” + a number like “%7C1211540101%7Cb954a41e23200ea6951bdeb405dc5237.”
Perhaps this is some kind of hash? I know WPMU 1.5.1 added a salt key to the wp-config.php file, so maybe that has something to do with it.
Thanks for the feedback. I was able to fix the problem by installing a plugin that allowed me to change where WPMU sets cookies. Everything is working correctly now!