When cloning a website that existed before the recent site manager upgrade, the tagline/subtitle field does not get transferred by the clone process. This results in the #header h2 not being displayed as per the recent bug http://feedback.wikidot.com/bug:808.
Also, I don't know if it is just a coincidence, but the first time I tried to clone my site I got an ajax error and the second time I got a wikidot error message saying that the clone process did not complete successfully. On both occasions the new site did exist, but without the #header h2 displayed and without a tagline transferred.
Thanks for reporting. Solved.