I am having this problem too, so I figured I would throw out my scenario and see if it helps.
I did a fresh install of 2.6 this morning as a subdomain setup. I set it up like this:
example.com
then 2 additional blogs:
other.example.com
other2.example.com
then I changed those values in the blog info page to:
other.com
other2.com
both those domains are parked at example.com
my goal is to have the user other be able to access other.com and example.com, and the user other2 to access other2.com and example.com.
it is redirecting with the correct site, and i can log in at example.com/wp-login, but switching to one of the other dashboards or logging in from other.com/wp-login redirects back over and over and over.
any ideas?