Database doesn't recognize cloned sites as unique?

Hi,

I am pretty new to Multisite, but successfully set up and administered a network without a hitch for classroom blogs last year (July 2014, not sure which WP version that would have been). I tried to replicate the same process this year, but have run in to one persistent problem.

I did everything exactly the same way I did last year, and used NSCloner to duplicate a “model” site for each student. However, when the students log in their dashboard displays an error message at the top (everything else is normal). It’s a red box that reads “It looks like you may have changed your domain. Is https://www.sitename.org/subdomain-1 still your site’s domain, or have you updated it to https://www.sitename.org/subdomain-2?”

Whether I ignore it or click on “update”, nothing seems to change– the same error message appears on the next sub-site I visit. However, a couple of students (not all!) have reported that changes they’ve made to their blogs mysteriously disappear the next time they visit, and I suspect it may have something to do with whatever is causing this error message.

My best guess is that the database doesn’t recognize the cloned sites as unique? If that’s the case, how do I fix it?? If that’s not the case… then what’s going on?!

Thanks in advance for any help and advice!