I had the same problem - the SCANNING SITE message never cleared.
Taking the advise of deactiving some of the plugins, I went to my Plugin's management page and selected ALL the plugsin and hit DEACTIVATE. I then went back to the DUPLICATE plugin manager and it worked.
But here's when I noticed something very strange....
I went back to find out which plugin was causing the problem.
I re-actived a few plugin bit by bit at a time, then I went back to the Duplicate plugin to see whether or not it would still have problem scanning. Each batch of plugins still worked. After doing this about 15 times I realized that there weren't ANY plugins that had problems! They ALL were ACTIVED and working just fine.
I think just simply: #1) DEACTIVING all the plugins (except for Duplicate), then #2 go back to Duplicate and run a scan again (should work now) and then #3 going back to the plugin page to ACTIVATE everything again might just do the trick.
Good luck and fingers crossed!