Multisite with top-level domain issue after 3.1 upgrade

Hey Folks,

Prior to upgrading to 3.1 we had been able to run our blog network by choosing to add sites/blogs at the domains top-level (https://blogsite.com) or the sub-domain level (https://blogsite.fireemsblogs.com). I assume that of the 40 or so blogs on the network greater than 30 of them were added at the domains top level.

Since the upgrade the ability to add a site at the top domain level has been eliminated. I am assuming there is a file that needs to be tweaked, or a setting that I am missing, or a plugin that went rogue and am looking for some help figuring it out.

Any assistance you can provide would be appreciated.

Thanks
Chris