/etc/init.d/iptables don't keep counters information when saving or reloading configuration. This is problematic when relying on it for traffic graph for example. The problem doesn't only occur when rebooting, but also when iptables restart because of a dependencie with another service currently restarted. So, I suggest adding -c option to iptables-save and iptables-restore in /etc/init.d/iptables. Of course, adding a flag to select this behavior will be probably more interesting (but then, set it to 'on' by default.)
Fixed in -r2. Thanks for finding this!
