I thought I’d check in with a little update as well for anyone else finding this thread who’s experiencing the same issue.
My solution to the problem was to increase the PHP memory limit, it was 64M which apparently was not enough to completely create the duplicate and create the zip.
I just want to say thank you as well Cory, this plugin is a true lifesaver – Before I kept messing with complete FTP uploads which resulted in broken uploads after taking hours to complete. A complete move is now done in less then 5 minutes, so I can hardly explain how happy I am with this plugin!