Thank you for using Ubuntu and filing a bug. The behavior you describe
is actually be design, but is configurable. Many applications will add
firewall rules to the various default chains. This is done without the
ufw cli command or the ufw framework. As such, performing a flush on
'reload' becomes a destructive operation and this is inappropriate in
the default installation. From /etc/default/ufw:

# By default, ufw only touches its own chains. Set this to 'yes' to have ufw
# manage the built-in chains too. Warning: setting this to 'yes' will break
# non-ufw managed firewall rules
MANAGE_BUILTINS=no

So if you would prefer this behavior, set MANAGE_BUILTINS=yes

** Changed in: ufw (Ubuntu)
       Status: New => Won't Fix

** Changed in: ufw (Ubuntu)
     Assignee: Jamie Strandboge (jdstrand) => (unassigned)

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https://bugs.launchpad.net/bugs/881137

Title:
  UFW does not clean iptables setting from /etc/ufw/before.rules

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