If you have vast experience running ntop and Debian derived distributions, you would intuit the need to consult /usr/share/doc/ntop/README.Debian, where they duely instruct you to run sudo ntop -A before running sudo /etc/init.d/ntop start. "ntop -A" queries you for the administrative password, and initializes /var/lib/ntop with various files. Ordinary mortals just starting out with ntop may be forgiven for overlooking this. It's probably the source of your directory and permissions issues, as a side effect.
The default settings for ntop are fairly good; if you have no need to tamper with them, be happy. I'm not sure if you can re-initialize ntop easily after the fact. If you are willing to reinstall it, which will lose the current DB contents, what I'd suggest is:
Code:
sudo -i
/etc/init.d/ntop stop
apt-get purge ntop
apt-get install ntop
ntop -A
/etc/init.d/ntop start
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