The multiserver setup still utilises the cron jobs running to process tasks sent. So until the jobqueue is processed the site will show but the necessary structure won't be created. Is your cron daemon running?
Have a look in your ispconfig control panel under monitor, see if there are any jobs stuck in the queue?
I believe you could manually run the command that's scheduled in the crontab without piping it to null, will spit any output including errors on the screen:
which should process any tasks same as cron job. If it doesn't it might give you pointer as to why not.
I just built a multiserver here on CentOS 6.4 x64 and both master and slave created test sites correctly.