After upgrading to 3.1.1, the categories of our sub-directory sites in the Network are displaying the category list of the main (ID=1) site. On the front end, the published posts are fine, and show each site's unique set of categories, but on the backend for each site, the categories are incorrect.
For example, this post: http://www.rockbrookcamp.com/alumnae/blog/elizabeth-oneill-verner.html has the category "history," but if we edit that post, it switches to the default category of the main site ("summer camp").
So the front end seems to be working fine, but the backend is confused between sites in the network.
Ideas where I can look? There don't seem to be any site errors.