Hey. I'm using an rpi2 as an OpenVPN bridge, so I have ip_forwarding enabled and a MASQUERADE target for packets leaving the tun interface. I have an entry in /etc/sysctl.d, rules in /etc/iptables/iptables.rules, and iptables.service enabled which calls iptables-restore.
I found this old thread which may be related. At first glance, on my system, ip_forwarding isn't working. Eventually I realized it stops working after iptables rules are reloaded.
A fix is simply to disable (write 0 to ip_forward) and then re-enable (write 1). I haven't encountered this issue on any other system, so I don't know if it's a race condition that I'm only seeing now on the pi, or there's something specific to this system.