I have cloned a site per the instructions and all seems to be working well except that the menus aren’t working. I’ve checked all the basics – Theme Location setting, resaving Permalinks, to no avail. I’ve also tried some some basic wp_page_menu arrays to see if I can get any list of pages to appear and its empty everytime.
I did not first deactivate all the plugins on the original site before cloning it. 1) I don’t think that should be necessary. 2) I didn’t see that in the plugin instructions. 3) i can’t really do it anyway, since it’s a live site.