Yes, I believe I deleted the records I added before the I re-ran the adds. Sorry - my memory is a little hazy; it was over two years ago when I was doing this.
Hey, I never got a legitimate solution to this problem. I believe I wound up doing 100 domains at a time and waiting a few minutes between running the commands.
I've added 400 domains via the command line to avoid having to do it manually in the web interface. Every domain was added with this formula:
./domain --create domain.info -clogin admin -status enabled -hosting true -hst_type phys -ip myip -login domain -passwd mypw -cgi false -php true -www...