Hai,
When i upgrade,i was always having following:
Warning! Problem upgrading . Your server may not be able to connect to blogs running on it.
Error message: malformed
So what i did is always skip the blog url that have problem.I just modify the url.Just retype proceed forward number at the xxxx.This is what i did so can continue upgrade all the blogs with out waste time.
wp-admin/wpmu-upgrade-site.php?action=upgrade&n=XXXX
So,it was very time consuming actually which i have more than 3000 blogs.It will be nice if can able to skip and generate report later about which blog was having error during upgrade