Something trouble with your /home/apache dir. This dir not standard dir but symlink from /var/lib/mysql/apache.
I was already fix issue and ready for running fixweb.
In my test on my kvm 1gb ram, create 2000 domains need 70 minutes (around 2 seconds/domains). Remember, create domains not only create web config but also create dns config, mail config (postmaster account) and etc.
My predictions, estimate time for fixweb are 1 domains/second.