Cloner is stuck

I'm using the cloner to make some staging sites on our network and it's worked well so far. Really like it! However, I got brave and tried it with a domain that is using the "Domains Mapping" ability from you guys. I couldn't find anything in the forums that would suggest it wouldn't work, but it seems to be stuck. I just see a spinning wheel that say "Please wait..." It does say it copied the settings but nothing else seems to be working. It's been stuck for at least 20 minutes. Should I just be patient or does it not work in this case?