Do NOT run xsitecopy as root. My experience has shown that for some reason all the sanity tests that determine (for example) whether a site is selected when you click certain buttons, just fail inexplicably.
Once a new site has been created, the site's "statistics" seem to occasionally be wrong. Restarting the program seems to correct that. I *think* this is now fixed, but if you still encounter the problem, please let me know.