Main domain on multisite configured

I have a new install of multisite hosted on Psek. The primary domain, thriveonlinedesign.com, has a strange initial set up of the permalinks that is causing problems. Everything is routing through a blog folder that I didn't set up and don't want. http://thriveonlinedesign.com/blog/%postname%/

I added another site to the multisite to see if this was some strange artifact of multisite. But no--that one has the normal configuration that I've seen with all other Wordpress installs: http://thriveonlinedesign.com/balance-demo/%postname%/

Any idea why this configuration would happen and what I can do to remove it? It is messing with my template and my portfolio settings. BTW, I can install the same template on the other theme and get the proper structure.