First off, LOVE the plugin! I did run into 1 problem, could be just me though.
If have a site X on domain 1, I duplicated and installed that site on domain 2.
Everything seemed to work, but when I go back to domain 1, the site now automatically directs to domain 2... which is quite odd because I didn't change any files on domain 1, only created the package and downloaded it.
The 2 domains are on the same hosting account tho (hostgator).